EndPoints hormonal treatments - CTL08
Date: July 22, 2025
Purpose
Compare the DEGs obtained across time points and produce related visualizations.
Approaches
Basic DEA vs DMSO
- Overlap of genes modulated by Agonist treatment vs DMSO (split in up-reg and down-reg) - section 3
- Overlap of genes modulated by Inhibitor treatment vs DMSO (split in up-reg and down-reg) - section 4
- Overlap of up-regulated genes induced by treatment vs DMSO (either agonist or antagonist) - section 5
- Overlap of down-regulated genes induced by treatment vs DMSO (either agonist or antagonist) - section 6
Basic DEA Agonist vs Inhibitor
- Overlap of genes modulated by Agonist treatment vs Inhibitor (split in up-reg and down-reg) - section 7
Analyses are performed for all pathways or a selected subset (estrogen, retionic, thyroid, liverX).
1. Environment SetUp
library(tidyr)
library(dplyr)
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library(ggplot2)
library(GeneOverlap)
OutputFolder <- params$OutputFolder2. Data Upload
DEA analysis with SeqRun as co-variable.
DEA <- readRDS(paste0(params$InputFolder, 'DEARes.rds'))3. Comparison across pathways: treatment with Agonist
3.1 Perform Overlap
DEGs_Agonist <- list(
Thyr_Ag_Up= row.names(DEA$Thyr$Agonist$DEGs[DEA$Thyr$Agonist$DEGs$log2FoldChange > 0, ]),
Thyr_Ag_Down= row.names(DEA$Thyr$Agonist$DEGs[DEA$Thyr$Agonist$DEGs$log2FoldChange < 0, ]),
Ret_Ag_Up= row.names(DEA$Ret$Agonist$DEGs[DEA$Ret$Agonist$DEGs$log2FoldChange > 0, ]),
Ret_Ag_Down= row.names(DEA$Ret$Agonist$DEGs[DEA$Ret$Agonist$DEGs$log2FoldChange < 0, ]),
Estr_Ag_Up= row.names(DEA$Estr$Agonist$DEGs[DEA$Estr$Agonist$DEGs$log2FoldChange > 0, ]),
Estr_Ag_Down= row.names(DEA$Estr$Agonist$DEGs[DEA$Estr$Agonist$DEGs$log2FoldChange < 0, ]),
Andr_Ag_Up= row.names(DEA$Andr$Agonist$DEGs[DEA$Andr$Agonist$DEGs$log2FoldChange > 0, ]),
Andr_Ag_Down= row.names(DEA$Andr$Agonist$DEGs[DEA$Andr$Agonist$DEGs$log2FoldChange < 0, ]),
GC_Ag_Up= row.names(DEA$GC$Agonist$DEGs[DEA$GC$Agonist$DEGs$log2FoldChange > 0, ]),
GC_Ag_Down= row.names(DEA$GC$Agonist$DEGs[DEA$GC$Agonist$DEGs$log2FoldChange < 0, ]),
LivX_Ag_Up= row.names(DEA$LivX$Agonist$DEGs[DEA$LivX$Agonist$DEGs$log2FoldChange > 0, ]),
LivX_Ag_Down= row.names(DEA$LivX$Agonist$DEGs[DEA$LivX$Agonist$DEGs$log2FoldChange < 0, ]),
AhHyd_Ag_Up= row.names(DEA$AhHyd$Agonist$DEGs[DEA$AhHyd$Agonist$DEGs$log2FoldChange > 0, ]),
AhHyd_Ag_Down= row.names(DEA$AhHyd$Agonist$DEGs[DEA$AhHyd$Agonist$DEGs$log2FoldChange < 0, ])
)Universe <- row.names(DEA$Ret$Agonist$Res) %>% unique()
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length(Universe)
## [1] 14850OvObj <- newGOM(DEGs_Agonist, DEGs_Agonist, genome.size=length(Universe))
print(OvObj)
## A GeneOverlapMatrix object:
## ###### Intersection ######
## Thyr_Ag_Up Thyr_Ag_Down Ret_Ag_Up Ret_Ag_Down Estr_Ag_Up
## Thyr_Ag_Up 142 0 81 14 84
## Thyr_Ag_Down 0 22 3 2 0
## Ret_Ag_Up 81 3 1677 0 462
## Ret_Ag_Down 14 2 0 1369 21
## Estr_Ag_Up 84 0 462 21 905
## Estr_Ag_Down 1 8 26 401 0
## Andr_Ag_Up 5 0 4 1 4
## Andr_Ag_Down 0 1 0 1 0
## GC_Ag_Up 0 0 1 2 1
## GC_Ag_Down 0 0 0 0 0
## LivX_Ag_Up 56 1 367 7 219
## LivX_Ag_Down 0 0 5 210 2
## AhHyd_Ag_Up 0 0 0 0 0
## AhHyd_Ag_Down 0 12 21 2 9
## Estr_Ag_Down Andr_Ag_Up Andr_Ag_Down GC_Ag_Up GC_Ag_Down
## Thyr_Ag_Up 1 5 0 0 0
## Thyr_Ag_Down 8 0 1 0 0
## Ret_Ag_Up 26 4 0 1 0
## Ret_Ag_Down 401 1 1 2 0
## Estr_Ag_Up 0 4 0 1 0
## Estr_Ag_Down 797 0 2 1 1
## Andr_Ag_Up 0 6 0 0 0
## Andr_Ag_Down 2 0 4 0 0
## GC_Ag_Up 1 0 0 6 0
## GC_Ag_Down 1 0 0 0 3
## LivX_Ag_Up 3 5 0 0 0
## LivX_Ag_Down 72 0 1 0 1
## AhHyd_Ag_Up 0 0 0 0 0
## AhHyd_Ag_Down 9 0 1 0 0
## LivX_Ag_Up LivX_Ag_Down AhHyd_Ag_Up AhHyd_Ag_Down
## Thyr_Ag_Up 56 0 0 0
## Thyr_Ag_Down 1 0 0 12
## Ret_Ag_Up 367 5 0 21
## Ret_Ag_Down 7 210 0 2
## Estr_Ag_Up 219 2 0 9
## Estr_Ag_Down 3 72 0 9
## Andr_Ag_Up 5 0 0 0
## Andr_Ag_Down 0 1 0 1
## GC_Ag_Up 0 0 0 0
## GC_Ag_Down 0 1 0 0
## LivX_Ag_Up 450 0 0 5
## LivX_Ag_Down 0 383 0 1
## AhHyd_Ag_Up 0 0 3 0
## AhHyd_Ag_Down 5 1 0 58
## ###### P-value ######
## Thyr_Ag_Up Thyr_Ag_Down Ret_Ag_Up Ret_Ag_Down
## Thyr_Ag_Up 0.000000e+00 1.000000e+00 3.063677e-40 4.373418e-01
## Thyr_Ag_Down 1.000000e+00 1.903459e-71 4.596806e-01 6.150185e-01
## Ret_Ag_Up 3.063677e-40 4.596806e-01 0.000000e+00 1.000000e+00
## Ret_Ag_Down 4.373418e-01 6.150185e-01 1.000000e+00 0.000000e+00
## Estr_Ag_Up 2.641447e-65 1.000000e+00 3.762356e-212 1.000000e+00
## Estr_Ag_Down 9.996186e-01 1.083997e-05 1.000000e+00 1.370389e-215
## Andr_Ag_Up 4.435963e-10 1.000000e+00 2.013961e-03 4.403334e-01
## Andr_Ag_Down 1.000000e+00 5.913366e-03 1.000000e+00 3.208514e-01
## GC_Ag_Up 1.000000e+00 1.000000e+00 5.128154e-01 9.920095e-02
## GC_Ag_Down 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## LivX_Ag_Up 4.556114e-48 4.920961e-01 1.730574e-276 1.000000e+00
## LivX_Ag_Down 1.000000e+00 1.000000e+00 1.000000e+00 6.406226e-118
## AhHyd_Ag_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## AhHyd_Ag_Down 1.000000e+00 2.344408e-24 6.035614e-07 9.749612e-01
## Estr_Ag_Up Estr_Ag_Down Andr_Ag_Up Andr_Ag_Down
## Thyr_Ag_Up 2.641447e-65 9.996186e-01 4.435963e-10 1.000000e+00
## Thyr_Ag_Down 1.000000e+00 1.083997e-05 1.000000e+00 5.913366e-03
## Ret_Ag_Up 3.762356e-212 1.000000e+00 2.013961e-03 1.000000e+00
## Ret_Ag_Down 1.000000e+00 1.370389e-215 4.403334e-01 3.208514e-01
## Estr_Ag_Up 0.000000e+00 1.000000e+00 1.861609e-04 1.000000e+00
## Estr_Ag_Down 1.000000e+00 0.000000e+00 1.000000e+00 1.605467e-02
## Andr_Ag_Up 1.861609e-04 1.000000e+00 6.720669e-23 1.000000e+00
## Andr_Ag_Down 1.000000e+00 1.605467e-02 1.000000e+00 4.937202e-16
## GC_Ag_Up 3.143162e-01 2.818244e-01 1.000000e+00 1.000000e+00
## GC_Ag_Down 1.000000e+00 1.525330e-01 1.000000e+00 1.000000e+00
## LivX_Ag_Up 1.688829e-149 1.000000e+00 1.462864e-07 1.000000e+00
## LivX_Ag_Down 1.000000e+00 3.359345e-21 1.000000e+00 9.925167e-02
## AhHyd_Ag_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## AhHyd_Ag_Down 8.022330e-03 3.526989e-03 1.000000e+00 1.553317e-02
## GC_Ag_Up GC_Ag_Down LivX_Ag_Up LivX_Ag_Down
## Thyr_Ag_Up 1.000000e+00 1.000000e+00 4.556114e-48 1.000000e+00
## Thyr_Ag_Down 1.000000e+00 1.000000e+00 4.920961e-01 1.000000e+00
## Ret_Ag_Up 5.128154e-01 1.000000e+00 1.730574e-276 1.000000e+00
## Ret_Ag_Down 9.920095e-02 1.000000e+00 1.000000e+00 6.406226e-118
## Estr_Ag_Up 3.143162e-01 1.000000e+00 1.688829e-149 1.000000e+00
## Estr_Ag_Down 2.818244e-01 1.525330e-01 1.000000e+00 3.359345e-21
## Andr_Ag_Up 1.000000e+00 1.000000e+00 1.462864e-07 1.000000e+00
## Andr_Ag_Down 1.000000e+00 1.000000e+00 1.000000e+00 9.925167e-02
## GC_Ag_Up 6.720669e-23 1.000000e+00 1.000000e+00 1.000000e+00
## GC_Ag_Down 1.000000e+00 1.832566e-12 1.000000e+00 7.540027e-02
## LivX_Ag_Up 1.000000e+00 1.000000e+00 0.000000e+00 1.000000e+00
## LivX_Ag_Down 1.000000e+00 7.540027e-02 1.000000e+00 0.000000e+00
## AhHyd_Ag_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## AhHyd_Ag_Down 1.000000e+00 1.000000e+00 3.077775e-02 7.809545e-01
## AhHyd_Ag_Up AhHyd_Ag_Down
## Thyr_Ag_Up 1.000000e+00 1.000000e+00
## Thyr_Ag_Down 1.000000e+00 2.344408e-24
## Ret_Ag_Up 1.000000e+00 6.035614e-07
## Ret_Ag_Down 1.000000e+00 9.749612e-01
## Estr_Ag_Up 1.000000e+00 8.022330e-03
## Estr_Ag_Down 1.000000e+00 3.526989e-03
## Andr_Ag_Up 1.000000e+00 1.000000e+00
## Andr_Ag_Down 1.000000e+00 1.553317e-02
## GC_Ag_Up 1.000000e+00 1.000000e+00
## GC_Ag_Down 1.000000e+00 1.000000e+00
## LivX_Ag_Up 1.000000e+00 3.077775e-02
## LivX_Ag_Down 1.000000e+00 7.809545e-01
## AhHyd_Ag_Up 1.832566e-12 1.000000e+00
## AhHyd_Ag_Down 1.000000e+00 2.880331e-164
## ###### Odds Ratio ######
## Thyr_Ag_Up Thyr_Ag_Down Ret_Ag_Up Ret_Ag_Down Estr_Ag_Up
## Thyr_Ag_Up Inf 0.0000000 10.9057151 1.0778737 24.46916321
## Thyr_Ag_Down 0.0000000 Inf 1.2406888 0.9847119 0.00000000
## Ret_Ag_Up 10.9057151 1.2406888 Inf 0.0000000 10.92340731
## Ret_Ag_Down 1.0778737 0.9847119 0.0000000 Inf 0.22200854
## Estr_Ag_Up 24.4691632 0.0000000 10.9234073 0.2220085 Inf
## Estr_Ag_Down 0.1239603 10.1637020 0.2533306 13.6832853 0.00000000
## Andr_Ag_Up 533.9879643 0.0000000 15.7395497 1.9701008 30.94356191
## Andr_Ag_Down 0.0000000 233.8786721 0.0000000 3.2836910 0.00000000
## GC_Ag_Up 0.0000000 0.0000000 1.5712909 4.9284852 3.08367430
## GC_Ag_Down 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
## LivX_Ag_Up 23.6359221 1.5248917 44.2014086 0.1512710 18.94632507
## LivX_Ag_Down 0.0000000 0.0000000 0.1012307 13.9349772 0.07884643
## AhHyd_Ag_Up 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
## AhHyd_Ag_Down 0.0000000 380.7075634 4.5016304 0.3507583 2.84825846
## Estr_Ag_Down Andr_Ag_Up Andr_Ag_Down GC_Ag_Up GC_Ag_Down
## Thyr_Ag_Up 0.1239603 533.987964 0.000000 0.000000 0.000000
## Thyr_Ag_Down 10.1637020 0.000000 233.878672 0.000000 0.000000
## Ret_Ag_Up 0.2533306 15.739550 0.000000 1.571291 0.000000
## Ret_Ag_Down 13.6832853 1.970101 3.283691 4.928485 0.000000
## Estr_Ag_Up 0.0000000 30.943562 0.000000 3.083674 0.000000
## Estr_Ag_Down Inf 0.000000 17.661478 3.529102 8.823612
## Andr_Ag_Up 0.0000000 Inf 0.000000 0.000000 0.000000
## Andr_Ag_Down 17.6614783 0.000000 Inf 0.000000 0.000000
## GC_Ag_Up 3.5291021 0.000000 0.000000 Inf 0.000000
## GC_Ag_Down 8.8236122 0.000000 0.000000 0.000000 Inf
## LivX_Ag_Up 0.1150142 161.910790 0.000000 0.000000 0.000000
## LivX_Ag_Down 4.3873765 0.000000 12.611124 0.000000 18.918890
## AhHyd_Ag_Up 0.0000000 0.000000 0.000000 0.000000 0.000000
## AhHyd_Ag_Down 3.2637058 0.000000 86.109402 0.000000 0.000000
## LivX_Ag_Up LivX_Ag_Down AhHyd_Ag_Up AhHyd_Ag_Down
## Thyr_Ag_Up 23.6359221 0.00000000 0 0.0000000
## Thyr_Ag_Down 1.5248917 0.00000000 0 380.7075634
## Ret_Ag_Up 44.2014086 0.10123069 0 4.5016304
## Ret_Ag_Down 0.1512710 13.93497718 0 0.3507583
## Estr_Ag_Up 18.9463251 0.07884643 0 2.8482585
## Estr_Ag_Down 0.1150142 4.38737655 0 3.2637058
## Andr_Ag_Up 161.9107898 0.00000000 0 0.0000000
## Andr_Ag_Down 0.0000000 12.61112374 0 86.1094022
## GC_Ag_Up 0.0000000 0.00000000 0 0.0000000
## GC_Ag_Down 0.0000000 18.91888965 0 0.0000000
## LivX_Ag_Up Inf 0.00000000 0 3.0411259
## LivX_Ag_Down 0.0000000 Inf 0 0.6618125
## AhHyd_Ag_Up 0.0000000 0.00000000 Inf 0.0000000
## AhHyd_Ag_Down 3.0411259 0.66181252 0 Inf
## ###### Jaccard Index ######
## Thyr_Ag_Up Thyr_Ag_Down Ret_Ag_Up Ret_Ag_Down Estr_Ag_Up
## Thyr_Ag_Up 1.000000000 0.000000000 0.0466052934 0.009352037 0.087227414
## Thyr_Ag_Down 0.000000000 1.000000000 0.0017688679 0.001439885 0.000000000
## Ret_Ag_Up 0.046605293 0.001768868 1.0000000000 0.000000000 0.217924528
## Ret_Ag_Down 0.009352037 0.001439885 0.0000000000 1.000000000 0.009320905
## Estr_Ag_Up 0.087227414 0.000000000 0.2179245283 0.009320905 1.000000000
## Estr_Ag_Down 0.001066098 0.009864365 0.0106209150 0.227195467 0.000000000
## Andr_Ag_Up 0.034965035 0.000000000 0.0023823705 0.000727802 0.004410143
## Andr_Ag_Down 0.000000000 0.040000000 0.0000000000 0.000728863 0.000000000
## GC_Ag_Up 0.000000000 0.000000000 0.0005945303 0.001456664 0.001098901
## GC_Ag_Down 0.000000000 0.000000000 0.0000000000 0.000000000 0.000000000
## LivX_Ag_Up 0.104477612 0.002123142 0.2085227273 0.003863135 0.192781690
## LivX_Ag_Down 0.000000000 0.000000000 0.0024330900 0.136186770 0.001555210
## AhHyd_Ag_Up 0.000000000 0.000000000 0.0000000000 0.000000000 0.000000000
## AhHyd_Ag_Down 0.000000000 0.176470588 0.0122520420 0.001403509 0.009433962
## Estr_Ag_Down Andr_Ag_Up Andr_Ag_Down GC_Ag_Up GC_Ag_Down
## Thyr_Ag_Up 0.001066098 0.034965035 0.000000000 0.0000000000 0.000000000
## Thyr_Ag_Down 0.009864365 0.000000000 0.040000000 0.0000000000 0.000000000
## Ret_Ag_Up 0.010620915 0.002382370 0.000000000 0.0005945303 0.000000000
## Ret_Ag_Down 0.227195467 0.000727802 0.000728863 0.0014566642 0.000000000
## Estr_Ag_Up 0.000000000 0.004410143 0.000000000 0.0010989011 0.000000000
## Estr_Ag_Down 1.000000000 0.000000000 0.002503129 0.0012468828 0.001251564
## Andr_Ag_Up 0.000000000 1.000000000 0.000000000 0.0000000000 0.000000000
## Andr_Ag_Down 0.002503129 0.000000000 1.000000000 0.0000000000 0.000000000
## GC_Ag_Up 0.001246883 0.000000000 0.000000000 1.0000000000 0.000000000
## GC_Ag_Down 0.001251564 0.000000000 0.000000000 0.0000000000 1.000000000
## LivX_Ag_Up 0.002411576 0.011086475 0.000000000 0.0000000000 0.000000000
## LivX_Ag_Down 0.064981949 0.000000000 0.002590674 0.0000000000 0.002597403
## AhHyd_Ag_Up 0.000000000 0.000000000 0.000000000 0.0000000000 0.000000000
## AhHyd_Ag_Down 0.010638298 0.000000000 0.016393443 0.0000000000 0.000000000
## LivX_Ag_Up LivX_Ag_Down AhHyd_Ag_Up AhHyd_Ag_Down
## Thyr_Ag_Up 0.104477612 0.000000000 0 0.000000000
## Thyr_Ag_Down 0.002123142 0.000000000 0 0.176470588
## Ret_Ag_Up 0.208522727 0.002433090 0 0.012252042
## Ret_Ag_Down 0.003863135 0.136186770 0 0.001403509
## Estr_Ag_Up 0.192781690 0.001555210 0 0.009433962
## Estr_Ag_Down 0.002411576 0.064981949 0 0.010638298
## Andr_Ag_Up 0.011086475 0.000000000 0 0.000000000
## Andr_Ag_Down 0.000000000 0.002590674 0 0.016393443
## GC_Ag_Up 0.000000000 0.000000000 0 0.000000000
## GC_Ag_Down 0.000000000 0.002597403 0 0.000000000
## LivX_Ag_Up 1.000000000 0.000000000 0 0.009940358
## LivX_Ag_Down 0.000000000 1.000000000 0 0.002272727
## AhHyd_Ag_Up 0.000000000 0.000000000 1 0.000000000
## AhHyd_Ag_Down 0.009940358 0.002272727 0 1.000000000getMatrix(OvObj, name='intersection')
## Thyr_Ag_Up Thyr_Ag_Down Ret_Ag_Up Ret_Ag_Down Estr_Ag_Up
## Thyr_Ag_Up 142 0 81 14 84
## Thyr_Ag_Down 0 22 3 2 0
## Ret_Ag_Up 81 3 1677 0 462
## Ret_Ag_Down 14 2 0 1369 21
## Estr_Ag_Up 84 0 462 21 905
## Estr_Ag_Down 1 8 26 401 0
## Andr_Ag_Up 5 0 4 1 4
## Andr_Ag_Down 0 1 0 1 0
## GC_Ag_Up 0 0 1 2 1
## GC_Ag_Down 0 0 0 0 0
## LivX_Ag_Up 56 1 367 7 219
## LivX_Ag_Down 0 0 5 210 2
## AhHyd_Ag_Up 0 0 0 0 0
## AhHyd_Ag_Down 0 12 21 2 9
## Estr_Ag_Down Andr_Ag_Up Andr_Ag_Down GC_Ag_Up GC_Ag_Down
## Thyr_Ag_Up 1 5 0 0 0
## Thyr_Ag_Down 8 0 1 0 0
## Ret_Ag_Up 26 4 0 1 0
## Ret_Ag_Down 401 1 1 2 0
## Estr_Ag_Up 0 4 0 1 0
## Estr_Ag_Down 797 0 2 1 1
## Andr_Ag_Up 0 6 0 0 0
## Andr_Ag_Down 2 0 4 0 0
## GC_Ag_Up 1 0 0 6 0
## GC_Ag_Down 1 0 0 0 3
## LivX_Ag_Up 3 5 0 0 0
## LivX_Ag_Down 72 0 1 0 1
## AhHyd_Ag_Up 0 0 0 0 0
## AhHyd_Ag_Down 9 0 1 0 0
## LivX_Ag_Up LivX_Ag_Down AhHyd_Ag_Up AhHyd_Ag_Down
## Thyr_Ag_Up 56 0 0 0
## Thyr_Ag_Down 1 0 0 12
## Ret_Ag_Up 367 5 0 21
## Ret_Ag_Down 7 210 0 2
## Estr_Ag_Up 219 2 0 9
## Estr_Ag_Down 3 72 0 9
## Andr_Ag_Up 5 0 0 0
## Andr_Ag_Down 0 1 0 1
## GC_Ag_Up 0 0 0 0
## GC_Ag_Down 0 1 0 0
## LivX_Ag_Up 450 0 0 5
## LivX_Ag_Down 0 383 0 1
## AhHyd_Ag_Up 0 0 3 0
## AhHyd_Ag_Down 5 1 0 58getMatrix(OvObj, name='pval')
## Thyr_Ag_Up Thyr_Ag_Down Ret_Ag_Up Ret_Ag_Down
## Thyr_Ag_Up 0.000000e+00 1.000000e+00 3.063677e-40 4.373418e-01
## Thyr_Ag_Down 1.000000e+00 1.903459e-71 4.596806e-01 6.150185e-01
## Ret_Ag_Up 3.063677e-40 4.596806e-01 0.000000e+00 1.000000e+00
## Ret_Ag_Down 4.373418e-01 6.150185e-01 1.000000e+00 0.000000e+00
## Estr_Ag_Up 2.641447e-65 1.000000e+00 3.762356e-212 1.000000e+00
## Estr_Ag_Down 9.996186e-01 1.083997e-05 1.000000e+00 1.370389e-215
## Andr_Ag_Up 4.435963e-10 1.000000e+00 2.013961e-03 4.403334e-01
## Andr_Ag_Down 1.000000e+00 5.913366e-03 1.000000e+00 3.208514e-01
## GC_Ag_Up 1.000000e+00 1.000000e+00 5.128154e-01 9.920095e-02
## GC_Ag_Down 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## LivX_Ag_Up 4.556114e-48 4.920961e-01 1.730574e-276 1.000000e+00
## LivX_Ag_Down 1.000000e+00 1.000000e+00 1.000000e+00 6.406226e-118
## AhHyd_Ag_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## AhHyd_Ag_Down 1.000000e+00 2.344408e-24 6.035614e-07 9.749612e-01
## Estr_Ag_Up Estr_Ag_Down Andr_Ag_Up Andr_Ag_Down
## Thyr_Ag_Up 2.641447e-65 9.996186e-01 4.435963e-10 1.000000e+00
## Thyr_Ag_Down 1.000000e+00 1.083997e-05 1.000000e+00 5.913366e-03
## Ret_Ag_Up 3.762356e-212 1.000000e+00 2.013961e-03 1.000000e+00
## Ret_Ag_Down 1.000000e+00 1.370389e-215 4.403334e-01 3.208514e-01
## Estr_Ag_Up 0.000000e+00 1.000000e+00 1.861609e-04 1.000000e+00
## Estr_Ag_Down 1.000000e+00 0.000000e+00 1.000000e+00 1.605467e-02
## Andr_Ag_Up 1.861609e-04 1.000000e+00 6.720669e-23 1.000000e+00
## Andr_Ag_Down 1.000000e+00 1.605467e-02 1.000000e+00 4.937202e-16
## GC_Ag_Up 3.143162e-01 2.818244e-01 1.000000e+00 1.000000e+00
## GC_Ag_Down 1.000000e+00 1.525330e-01 1.000000e+00 1.000000e+00
## LivX_Ag_Up 1.688829e-149 1.000000e+00 1.462864e-07 1.000000e+00
## LivX_Ag_Down 1.000000e+00 3.359345e-21 1.000000e+00 9.925167e-02
## AhHyd_Ag_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## AhHyd_Ag_Down 8.022330e-03 3.526989e-03 1.000000e+00 1.553317e-02
## GC_Ag_Up GC_Ag_Down LivX_Ag_Up LivX_Ag_Down
## Thyr_Ag_Up 1.000000e+00 1.000000e+00 4.556114e-48 1.000000e+00
## Thyr_Ag_Down 1.000000e+00 1.000000e+00 4.920961e-01 1.000000e+00
## Ret_Ag_Up 5.128154e-01 1.000000e+00 1.730574e-276 1.000000e+00
## Ret_Ag_Down 9.920095e-02 1.000000e+00 1.000000e+00 6.406226e-118
## Estr_Ag_Up 3.143162e-01 1.000000e+00 1.688829e-149 1.000000e+00
## Estr_Ag_Down 2.818244e-01 1.525330e-01 1.000000e+00 3.359345e-21
## Andr_Ag_Up 1.000000e+00 1.000000e+00 1.462864e-07 1.000000e+00
## Andr_Ag_Down 1.000000e+00 1.000000e+00 1.000000e+00 9.925167e-02
## GC_Ag_Up 6.720669e-23 1.000000e+00 1.000000e+00 1.000000e+00
## GC_Ag_Down 1.000000e+00 1.832566e-12 1.000000e+00 7.540027e-02
## LivX_Ag_Up 1.000000e+00 1.000000e+00 0.000000e+00 1.000000e+00
## LivX_Ag_Down 1.000000e+00 7.540027e-02 1.000000e+00 0.000000e+00
## AhHyd_Ag_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## AhHyd_Ag_Down 1.000000e+00 1.000000e+00 3.077775e-02 7.809545e-01
## AhHyd_Ag_Up AhHyd_Ag_Down
## Thyr_Ag_Up 1.000000e+00 1.000000e+00
## Thyr_Ag_Down 1.000000e+00 2.344408e-24
## Ret_Ag_Up 1.000000e+00 6.035614e-07
## Ret_Ag_Down 1.000000e+00 9.749612e-01
## Estr_Ag_Up 1.000000e+00 8.022330e-03
## Estr_Ag_Down 1.000000e+00 3.526989e-03
## Andr_Ag_Up 1.000000e+00 1.000000e+00
## Andr_Ag_Down 1.000000e+00 1.553317e-02
## GC_Ag_Up 1.000000e+00 1.000000e+00
## GC_Ag_Down 1.000000e+00 1.000000e+00
## LivX_Ag_Up 1.000000e+00 3.077775e-02
## LivX_Ag_Down 1.000000e+00 7.809545e-01
## AhHyd_Ag_Up 1.832566e-12 1.000000e+00
## AhHyd_Ag_Down 1.000000e+00 2.880331e-164getMatrix(OvObj, name='odds.ratio')
## Thyr_Ag_Up Thyr_Ag_Down Ret_Ag_Up Ret_Ag_Down Estr_Ag_Up
## Thyr_Ag_Up Inf 0.0000000 10.9057151 1.0778737 24.46916321
## Thyr_Ag_Down 0.0000000 Inf 1.2406888 0.9847119 0.00000000
## Ret_Ag_Up 10.9057151 1.2406888 Inf 0.0000000 10.92340731
## Ret_Ag_Down 1.0778737 0.9847119 0.0000000 Inf 0.22200854
## Estr_Ag_Up 24.4691632 0.0000000 10.9234073 0.2220085 Inf
## Estr_Ag_Down 0.1239603 10.1637020 0.2533306 13.6832853 0.00000000
## Andr_Ag_Up 533.9879643 0.0000000 15.7395497 1.9701008 30.94356191
## Andr_Ag_Down 0.0000000 233.8786721 0.0000000 3.2836910 0.00000000
## GC_Ag_Up 0.0000000 0.0000000 1.5712909 4.9284852 3.08367430
## GC_Ag_Down 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
## LivX_Ag_Up 23.6359221 1.5248917 44.2014086 0.1512710 18.94632507
## LivX_Ag_Down 0.0000000 0.0000000 0.1012307 13.9349772 0.07884643
## AhHyd_Ag_Up 0.0000000 0.0000000 0.0000000 0.0000000 0.00000000
## AhHyd_Ag_Down 0.0000000 380.7075634 4.5016304 0.3507583 2.84825846
## Estr_Ag_Down Andr_Ag_Up Andr_Ag_Down GC_Ag_Up GC_Ag_Down
## Thyr_Ag_Up 0.1239603 533.987964 0.000000 0.000000 0.000000
## Thyr_Ag_Down 10.1637020 0.000000 233.878672 0.000000 0.000000
## Ret_Ag_Up 0.2533306 15.739550 0.000000 1.571291 0.000000
## Ret_Ag_Down 13.6832853 1.970101 3.283691 4.928485 0.000000
## Estr_Ag_Up 0.0000000 30.943562 0.000000 3.083674 0.000000
## Estr_Ag_Down Inf 0.000000 17.661478 3.529102 8.823612
## Andr_Ag_Up 0.0000000 Inf 0.000000 0.000000 0.000000
## Andr_Ag_Down 17.6614783 0.000000 Inf 0.000000 0.000000
## GC_Ag_Up 3.5291021 0.000000 0.000000 Inf 0.000000
## GC_Ag_Down 8.8236122 0.000000 0.000000 0.000000 Inf
## LivX_Ag_Up 0.1150142 161.910790 0.000000 0.000000 0.000000
## LivX_Ag_Down 4.3873765 0.000000 12.611124 0.000000 18.918890
## AhHyd_Ag_Up 0.0000000 0.000000 0.000000 0.000000 0.000000
## AhHyd_Ag_Down 3.2637058 0.000000 86.109402 0.000000 0.000000
## LivX_Ag_Up LivX_Ag_Down AhHyd_Ag_Up AhHyd_Ag_Down
## Thyr_Ag_Up 23.6359221 0.00000000 0 0.0000000
## Thyr_Ag_Down 1.5248917 0.00000000 0 380.7075634
## Ret_Ag_Up 44.2014086 0.10123069 0 4.5016304
## Ret_Ag_Down 0.1512710 13.93497718 0 0.3507583
## Estr_Ag_Up 18.9463251 0.07884643 0 2.8482585
## Estr_Ag_Down 0.1150142 4.38737655 0 3.2637058
## Andr_Ag_Up 161.9107898 0.00000000 0 0.0000000
## Andr_Ag_Down 0.0000000 12.61112374 0 86.1094022
## GC_Ag_Up 0.0000000 0.00000000 0 0.0000000
## GC_Ag_Down 0.0000000 18.91888965 0 0.0000000
## LivX_Ag_Up Inf 0.00000000 0 3.0411259
## LivX_Ag_Down 0.0000000 Inf 0 0.6618125
## AhHyd_Ag_Up 0.0000000 0.00000000 Inf 0.0000000
## AhHyd_Ag_Down 3.0411259 0.66181252 0 Inf3.2 Visualize overlap results
DotPlot: data preparation
OR <- data.frame(getMatrix(OvObj, name='odds.ratio'))
OR$DEGs <- row.names(OR)
OR <- gather(OR, 'KBase', 'OR', -DEGs)
PVAL <- data.frame(getMatrix(OvObj, name='pval'))
PVAL$DEGs <- row.names(PVAL)
PVAL <- gather(PVAL, 'KBase', 'PVal', -DEGs)
NUM <- data.frame(getMatrix(OvObj, name='intersection'))
NUM$DEGs <- row.names(NUM)
NUM <- gather(NUM, 'KBase', 'Numbers', -DEGs)
if(! identical(OR$DEGs, PVAL$DEGs)){
stop('Inconsistecy')
}
if(! identical(OR$DEGs, NUM$DEGs)){
stop('Inconsistecy')
}
if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}
if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}
Res <- mutate(OR, Pval=PVAL$PVal) %>% mutate(Numbers=NUM$Numbers)
Res
## DEGs KBase OR Pval Numbers
## 1 Thyr_Ag_Up Thyr_Ag_Up Inf 0.000000e+00 142
## 2 Thyr_Ag_Down Thyr_Ag_Up 0.00000000 1.000000e+00 0
## 3 Ret_Ag_Up Thyr_Ag_Up 10.90571508 3.063677e-40 81
## 4 Ret_Ag_Down Thyr_Ag_Up 1.07787369 4.373418e-01 14
## 5 Estr_Ag_Up Thyr_Ag_Up 24.46916321 2.641447e-65 84
## 6 Estr_Ag_Down Thyr_Ag_Up 0.12396030 9.996186e-01 1
## 7 Andr_Ag_Up Thyr_Ag_Up 533.98796429 4.435963e-10 5
## 8 Andr_Ag_Down Thyr_Ag_Up 0.00000000 1.000000e+00 0
## 9 GC_Ag_Up Thyr_Ag_Up 0.00000000 1.000000e+00 0
## 10 GC_Ag_Down Thyr_Ag_Up 0.00000000 1.000000e+00 0
## 11 LivX_Ag_Up Thyr_Ag_Up 23.63592207 4.556114e-48 56
## 12 LivX_Ag_Down Thyr_Ag_Up 0.00000000 1.000000e+00 0
## 13 AhHyd_Ag_Up Thyr_Ag_Up 0.00000000 1.000000e+00 0
## 14 AhHyd_Ag_Down Thyr_Ag_Up 0.00000000 1.000000e+00 0
## 15 Thyr_Ag_Up Thyr_Ag_Down 0.00000000 1.000000e+00 0
## 16 Thyr_Ag_Down Thyr_Ag_Down Inf 1.903459e-71 22
## 17 Ret_Ag_Up Thyr_Ag_Down 1.24068882 4.596806e-01 3
## 18 Ret_Ag_Down Thyr_Ag_Down 0.98471188 6.150185e-01 2
## 19 Estr_Ag_Up Thyr_Ag_Down 0.00000000 1.000000e+00 0
## 20 Estr_Ag_Down Thyr_Ag_Down 10.16370202 1.083997e-05 8
## 21 Andr_Ag_Up Thyr_Ag_Down 0.00000000 1.000000e+00 0
## 22 Andr_Ag_Down Thyr_Ag_Down 233.87867212 5.913366e-03 1
## 23 GC_Ag_Up Thyr_Ag_Down 0.00000000 1.000000e+00 0
## 24 GC_Ag_Down Thyr_Ag_Down 0.00000000 1.000000e+00 0
## 25 LivX_Ag_Up Thyr_Ag_Down 1.52489175 4.920961e-01 1
## 26 LivX_Ag_Down Thyr_Ag_Down 0.00000000 1.000000e+00 0
## 27 AhHyd_Ag_Up Thyr_Ag_Down 0.00000000 1.000000e+00 0
## 28 AhHyd_Ag_Down Thyr_Ag_Down 380.70756337 2.344408e-24 12
## 29 Thyr_Ag_Up Ret_Ag_Up 10.90571508 3.063677e-40 81
## 30 Thyr_Ag_Down Ret_Ag_Up 1.24068882 4.596806e-01 3
## 31 Ret_Ag_Up Ret_Ag_Up Inf 0.000000e+00 1677
## 32 Ret_Ag_Down Ret_Ag_Up 0.00000000 1.000000e+00 0
## 33 Estr_Ag_Up Ret_Ag_Up 10.92340731 3.762356e-212 462
## 34 Estr_Ag_Down Ret_Ag_Up 0.25333064 1.000000e+00 26
## 35 Andr_Ag_Up Ret_Ag_Up 15.73954967 2.013961e-03 4
## 36 Andr_Ag_Down Ret_Ag_Up 0.00000000 1.000000e+00 0
## 37 GC_Ag_Up Ret_Ag_Up 1.57129089 5.128154e-01 1
## 38 GC_Ag_Down Ret_Ag_Up 0.00000000 1.000000e+00 0
## 39 LivX_Ag_Up Ret_Ag_Up 44.20140863 1.730574e-276 367
## 40 LivX_Ag_Down Ret_Ag_Up 0.10123069 1.000000e+00 5
## 41 AhHyd_Ag_Up Ret_Ag_Up 0.00000000 1.000000e+00 0
## 42 AhHyd_Ag_Down Ret_Ag_Up 4.50163038 6.035614e-07 21
## 43 Thyr_Ag_Up Ret_Ag_Down 1.07787369 4.373418e-01 14
## 44 Thyr_Ag_Down Ret_Ag_Down 0.98471188 6.150185e-01 2
## 45 Ret_Ag_Up Ret_Ag_Down 0.00000000 1.000000e+00 0
## 46 Ret_Ag_Down Ret_Ag_Down Inf 0.000000e+00 1369
## 47 Estr_Ag_Up Ret_Ag_Down 0.22200854 1.000000e+00 21
## 48 Estr_Ag_Down Ret_Ag_Down 13.68328533 1.370389e-215 401
## 49 Andr_Ag_Up Ret_Ag_Down 1.97010077 4.403334e-01 1
## 50 Andr_Ag_Down Ret_Ag_Down 3.28369103 3.208514e-01 1
## 51 GC_Ag_Up Ret_Ag_Down 4.92848520 9.920095e-02 2
## 52 GC_Ag_Down Ret_Ag_Down 0.00000000 1.000000e+00 0
## 53 LivX_Ag_Up Ret_Ag_Down 0.15127105 1.000000e+00 7
## 54 LivX_Ag_Down Ret_Ag_Down 13.93497718 6.406226e-118 210
## 55 AhHyd_Ag_Up Ret_Ag_Down 0.00000000 1.000000e+00 0
## 56 AhHyd_Ag_Down Ret_Ag_Down 0.35075826 9.749612e-01 2
## 57 Thyr_Ag_Up Estr_Ag_Up 24.46916321 2.641447e-65 84
## 58 Thyr_Ag_Down Estr_Ag_Up 0.00000000 1.000000e+00 0
## 59 Ret_Ag_Up Estr_Ag_Up 10.92340731 3.762356e-212 462
## 60 Ret_Ag_Down Estr_Ag_Up 0.22200854 1.000000e+00 21
## 61 Estr_Ag_Up Estr_Ag_Up Inf 0.000000e+00 905
## 62 Estr_Ag_Down Estr_Ag_Up 0.00000000 1.000000e+00 0
## 63 Andr_Ag_Up Estr_Ag_Up 30.94356191 1.861609e-04 4
## 64 Andr_Ag_Down Estr_Ag_Up 0.00000000 1.000000e+00 0
## 65 GC_Ag_Up Estr_Ag_Up 3.08367430 3.143162e-01 1
## 66 GC_Ag_Down Estr_Ag_Up 0.00000000 1.000000e+00 0
## 67 LivX_Ag_Up Estr_Ag_Up 18.94632507 1.688829e-149 219
## 68 LivX_Ag_Down Estr_Ag_Up 0.07884643 1.000000e+00 2
## 69 AhHyd_Ag_Up Estr_Ag_Up 0.00000000 1.000000e+00 0
## 70 AhHyd_Ag_Down Estr_Ag_Up 2.84825846 8.022330e-03 9
## 71 Thyr_Ag_Up Estr_Ag_Down 0.12396030 9.996186e-01 1
## 72 Thyr_Ag_Down Estr_Ag_Down 10.16370202 1.083997e-05 8
## 73 Ret_Ag_Up Estr_Ag_Down 0.25333064 1.000000e+00 26
## 74 Ret_Ag_Down Estr_Ag_Down 13.68328533 1.370389e-215 401
## 75 Estr_Ag_Up Estr_Ag_Down 0.00000000 1.000000e+00 0
## 76 Estr_Ag_Down Estr_Ag_Down Inf 0.000000e+00 797
## 77 Andr_Ag_Up Estr_Ag_Down 0.00000000 1.000000e+00 0
## 78 Andr_Ag_Down Estr_Ag_Down 17.66147826 1.605467e-02 2
## 79 GC_Ag_Up Estr_Ag_Down 3.52910210 2.818244e-01 1
## 80 GC_Ag_Down Estr_Ag_Down 8.82361218 1.525330e-01 1
## 81 LivX_Ag_Up Estr_Ag_Down 0.11501425 1.000000e+00 3
## 82 LivX_Ag_Down Estr_Ag_Down 4.38737655 3.359345e-21 72
## 83 AhHyd_Ag_Up Estr_Ag_Down 0.00000000 1.000000e+00 0
## 84 AhHyd_Ag_Down Estr_Ag_Down 3.26370576 3.526989e-03 9
## 85 Thyr_Ag_Up Andr_Ag_Up 533.98796429 4.435963e-10 5
## 86 Thyr_Ag_Down Andr_Ag_Up 0.00000000 1.000000e+00 0
## 87 Ret_Ag_Up Andr_Ag_Up 15.73954967 2.013961e-03 4
## 88 Ret_Ag_Down Andr_Ag_Up 1.97010077 4.403334e-01 1
## 89 Estr_Ag_Up Andr_Ag_Up 30.94356191 1.861609e-04 4
## 90 Estr_Ag_Down Andr_Ag_Up 0.00000000 1.000000e+00 0
## 91 Andr_Ag_Up Andr_Ag_Up Inf 6.720669e-23 6
## 92 Andr_Ag_Down Andr_Ag_Up 0.00000000 1.000000e+00 0
## 93 GC_Ag_Up Andr_Ag_Up 0.00000000 1.000000e+00 0
## 94 GC_Ag_Down Andr_Ag_Up 0.00000000 1.000000e+00 0
## 95 LivX_Ag_Up Andr_Ag_Up 161.91078980 1.462864e-07 5
## 96 LivX_Ag_Down Andr_Ag_Up 0.00000000 1.000000e+00 0
## 97 AhHyd_Ag_Up Andr_Ag_Up 0.00000000 1.000000e+00 0
## 98 AhHyd_Ag_Down Andr_Ag_Up 0.00000000 1.000000e+00 0
## 99 Thyr_Ag_Up Andr_Ag_Down 0.00000000 1.000000e+00 0
## 100 Thyr_Ag_Down Andr_Ag_Down 233.87867212 5.913366e-03 1
## 101 Ret_Ag_Up Andr_Ag_Down 0.00000000 1.000000e+00 0
## 102 Ret_Ag_Down Andr_Ag_Down 3.28369103 3.208514e-01 1
## 103 Estr_Ag_Up Andr_Ag_Down 0.00000000 1.000000e+00 0
## 104 Estr_Ag_Down Andr_Ag_Down 17.66147826 1.605467e-02 2
## 105 Andr_Ag_Up Andr_Ag_Down 0.00000000 1.000000e+00 0
## 106 Andr_Ag_Down Andr_Ag_Down Inf 4.937202e-16 4
## 107 GC_Ag_Up Andr_Ag_Down 0.00000000 1.000000e+00 0
## 108 GC_Ag_Down Andr_Ag_Down 0.00000000 1.000000e+00 0
## 109 LivX_Ag_Up Andr_Ag_Down 0.00000000 1.000000e+00 0
## 110 LivX_Ag_Down Andr_Ag_Down 12.61112374 9.925167e-02 1
## 111 AhHyd_Ag_Up Andr_Ag_Down 0.00000000 1.000000e+00 0
## 112 AhHyd_Ag_Down Andr_Ag_Down 86.10940218 1.553317e-02 1
## 113 Thyr_Ag_Up GC_Ag_Up 0.00000000 1.000000e+00 0
## 114 Thyr_Ag_Down GC_Ag_Up 0.00000000 1.000000e+00 0
## 115 Ret_Ag_Up GC_Ag_Up 1.57129089 5.128154e-01 1
## 116 Ret_Ag_Down GC_Ag_Up 4.92848520 9.920095e-02 2
## 117 Estr_Ag_Up GC_Ag_Up 3.08367430 3.143162e-01 1
## 118 Estr_Ag_Down GC_Ag_Up 3.52910210 2.818244e-01 1
## 119 Andr_Ag_Up GC_Ag_Up 0.00000000 1.000000e+00 0
## 120 Andr_Ag_Down GC_Ag_Up 0.00000000 1.000000e+00 0
## 121 GC_Ag_Up GC_Ag_Up Inf 6.720669e-23 6
## 122 GC_Ag_Down GC_Ag_Up 0.00000000 1.000000e+00 0
## 123 LivX_Ag_Up GC_Ag_Up 0.00000000 1.000000e+00 0
## 124 LivX_Ag_Down GC_Ag_Up 0.00000000 1.000000e+00 0
## 125 AhHyd_Ag_Up GC_Ag_Up 0.00000000 1.000000e+00 0
## 126 AhHyd_Ag_Down GC_Ag_Up 0.00000000 1.000000e+00 0
## 127 Thyr_Ag_Up GC_Ag_Down 0.00000000 1.000000e+00 0
## 128 Thyr_Ag_Down GC_Ag_Down 0.00000000 1.000000e+00 0
## 129 Ret_Ag_Up GC_Ag_Down 0.00000000 1.000000e+00 0
## 130 Ret_Ag_Down GC_Ag_Down 0.00000000 1.000000e+00 0
## 131 Estr_Ag_Up GC_Ag_Down 0.00000000 1.000000e+00 0
## 132 Estr_Ag_Down GC_Ag_Down 8.82361218 1.525330e-01 1
## 133 Andr_Ag_Up GC_Ag_Down 0.00000000 1.000000e+00 0
## 134 Andr_Ag_Down GC_Ag_Down 0.00000000 1.000000e+00 0
## 135 GC_Ag_Up GC_Ag_Down 0.00000000 1.000000e+00 0
## 136 GC_Ag_Down GC_Ag_Down Inf 1.832566e-12 3
## 137 LivX_Ag_Up GC_Ag_Down 0.00000000 1.000000e+00 0
## 138 LivX_Ag_Down GC_Ag_Down 18.91888965 7.540027e-02 1
## 139 AhHyd_Ag_Up GC_Ag_Down 0.00000000 1.000000e+00 0
## 140 AhHyd_Ag_Down GC_Ag_Down 0.00000000 1.000000e+00 0
## 141 Thyr_Ag_Up LivX_Ag_Up 23.63592207 4.556114e-48 56
## 142 Thyr_Ag_Down LivX_Ag_Up 1.52489175 4.920961e-01 1
## 143 Ret_Ag_Up LivX_Ag_Up 44.20140863 1.730574e-276 367
## 144 Ret_Ag_Down LivX_Ag_Up 0.15127105 1.000000e+00 7
## 145 Estr_Ag_Up LivX_Ag_Up 18.94632507 1.688829e-149 219
## 146 Estr_Ag_Down LivX_Ag_Up 0.11501425 1.000000e+00 3
## 147 Andr_Ag_Up LivX_Ag_Up 161.91078981 1.462864e-07 5
## 148 Andr_Ag_Down LivX_Ag_Up 0.00000000 1.000000e+00 0
## 149 GC_Ag_Up LivX_Ag_Up 0.00000000 1.000000e+00 0
## 150 GC_Ag_Down LivX_Ag_Up 0.00000000 1.000000e+00 0
## 151 LivX_Ag_Up LivX_Ag_Up Inf 0.000000e+00 450
## 152 LivX_Ag_Down LivX_Ag_Up 0.00000000 1.000000e+00 0
## 153 AhHyd_Ag_Up LivX_Ag_Up 0.00000000 1.000000e+00 0
## 154 AhHyd_Ag_Down LivX_Ag_Up 3.04112595 3.077775e-02 5
## 155 Thyr_Ag_Up LivX_Ag_Down 0.00000000 1.000000e+00 0
## 156 Thyr_Ag_Down LivX_Ag_Down 0.00000000 1.000000e+00 0
## 157 Ret_Ag_Up LivX_Ag_Down 0.10123069 1.000000e+00 5
## 158 Ret_Ag_Down LivX_Ag_Down 13.93497718 6.406226e-118 210
## 159 Estr_Ag_Up LivX_Ag_Down 0.07884643 1.000000e+00 2
## 160 Estr_Ag_Down LivX_Ag_Down 4.38737655 3.359345e-21 72
## 161 Andr_Ag_Up LivX_Ag_Down 0.00000000 1.000000e+00 0
## 162 Andr_Ag_Down LivX_Ag_Down 12.61112374 9.925167e-02 1
## 163 GC_Ag_Up LivX_Ag_Down 0.00000000 1.000000e+00 0
## 164 GC_Ag_Down LivX_Ag_Down 18.91888965 7.540027e-02 1
## 165 LivX_Ag_Up LivX_Ag_Down 0.00000000 1.000000e+00 0
## 166 LivX_Ag_Down LivX_Ag_Down Inf 0.000000e+00 383
## 167 AhHyd_Ag_Up LivX_Ag_Down 0.00000000 1.000000e+00 0
## 168 AhHyd_Ag_Down LivX_Ag_Down 0.66181252 7.809545e-01 1
## 169 Thyr_Ag_Up AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 170 Thyr_Ag_Down AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 171 Ret_Ag_Up AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 172 Ret_Ag_Down AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 173 Estr_Ag_Up AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 174 Estr_Ag_Down AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 175 Andr_Ag_Up AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 176 Andr_Ag_Down AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 177 GC_Ag_Up AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 178 GC_Ag_Down AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 179 LivX_Ag_Up AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 180 LivX_Ag_Down AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 181 AhHyd_Ag_Up AhHyd_Ag_Up Inf 1.832566e-12 3
## 182 AhHyd_Ag_Down AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 183 Thyr_Ag_Up AhHyd_Ag_Down 0.00000000 1.000000e+00 0
## 184 Thyr_Ag_Down AhHyd_Ag_Down 380.70756337 2.344408e-24 12
## 185 Ret_Ag_Up AhHyd_Ag_Down 4.50163038 6.035614e-07 21
## 186 Ret_Ag_Down AhHyd_Ag_Down 0.35075826 9.749612e-01 2
## 187 Estr_Ag_Up AhHyd_Ag_Down 2.84825846 8.022330e-03 9
## 188 Estr_Ag_Down AhHyd_Ag_Down 3.26370576 3.526989e-03 9
## 189 Andr_Ag_Up AhHyd_Ag_Down 0.00000000 1.000000e+00 0
## 190 Andr_Ag_Down AhHyd_Ag_Down 86.10940218 1.553317e-02 1
## 191 GC_Ag_Up AhHyd_Ag_Down 0.00000000 1.000000e+00 0
## 192 GC_Ag_Down AhHyd_Ag_Down 0.00000000 1.000000e+00 0
## 193 LivX_Ag_Up AhHyd_Ag_Down 3.04112595 3.077775e-02 5
## 194 LivX_Ag_Down AhHyd_Ag_Down 0.66181252 7.809545e-01 1
## 195 AhHyd_Ag_Up AhHyd_Ag_Down 0.00000000 1.000000e+00 0
## 196 AhHyd_Ag_Down AhHyd_Ag_Down Inf 2.880331e-164 58ResMod <- Res
ResMod[ResMod$DEGs == ResMod$KBase, ]$OR <- 1
ResMod[ResMod$DEGs == ResMod$KBase, ]$Pval <- 1
ResMod
## DEGs KBase OR Pval Numbers
## 1 Thyr_Ag_Up Thyr_Ag_Up 1.00000000 1.000000e+00 142
## 2 Thyr_Ag_Down Thyr_Ag_Up 0.00000000 1.000000e+00 0
## 3 Ret_Ag_Up Thyr_Ag_Up 10.90571508 3.063677e-40 81
## 4 Ret_Ag_Down Thyr_Ag_Up 1.07787369 4.373418e-01 14
## 5 Estr_Ag_Up Thyr_Ag_Up 24.46916321 2.641447e-65 84
## 6 Estr_Ag_Down Thyr_Ag_Up 0.12396030 9.996186e-01 1
## 7 Andr_Ag_Up Thyr_Ag_Up 533.98796429 4.435963e-10 5
## 8 Andr_Ag_Down Thyr_Ag_Up 0.00000000 1.000000e+00 0
## 9 GC_Ag_Up Thyr_Ag_Up 0.00000000 1.000000e+00 0
## 10 GC_Ag_Down Thyr_Ag_Up 0.00000000 1.000000e+00 0
## 11 LivX_Ag_Up Thyr_Ag_Up 23.63592207 4.556114e-48 56
## 12 LivX_Ag_Down Thyr_Ag_Up 0.00000000 1.000000e+00 0
## 13 AhHyd_Ag_Up Thyr_Ag_Up 0.00000000 1.000000e+00 0
## 14 AhHyd_Ag_Down Thyr_Ag_Up 0.00000000 1.000000e+00 0
## 15 Thyr_Ag_Up Thyr_Ag_Down 0.00000000 1.000000e+00 0
## 16 Thyr_Ag_Down Thyr_Ag_Down 1.00000000 1.000000e+00 22
## 17 Ret_Ag_Up Thyr_Ag_Down 1.24068882 4.596806e-01 3
## 18 Ret_Ag_Down Thyr_Ag_Down 0.98471188 6.150185e-01 2
## 19 Estr_Ag_Up Thyr_Ag_Down 0.00000000 1.000000e+00 0
## 20 Estr_Ag_Down Thyr_Ag_Down 10.16370202 1.083997e-05 8
## 21 Andr_Ag_Up Thyr_Ag_Down 0.00000000 1.000000e+00 0
## 22 Andr_Ag_Down Thyr_Ag_Down 233.87867212 5.913366e-03 1
## 23 GC_Ag_Up Thyr_Ag_Down 0.00000000 1.000000e+00 0
## 24 GC_Ag_Down Thyr_Ag_Down 0.00000000 1.000000e+00 0
## 25 LivX_Ag_Up Thyr_Ag_Down 1.52489175 4.920961e-01 1
## 26 LivX_Ag_Down Thyr_Ag_Down 0.00000000 1.000000e+00 0
## 27 AhHyd_Ag_Up Thyr_Ag_Down 0.00000000 1.000000e+00 0
## 28 AhHyd_Ag_Down Thyr_Ag_Down 380.70756337 2.344408e-24 12
## 29 Thyr_Ag_Up Ret_Ag_Up 10.90571508 3.063677e-40 81
## 30 Thyr_Ag_Down Ret_Ag_Up 1.24068882 4.596806e-01 3
## 31 Ret_Ag_Up Ret_Ag_Up 1.00000000 1.000000e+00 1677
## 32 Ret_Ag_Down Ret_Ag_Up 0.00000000 1.000000e+00 0
## 33 Estr_Ag_Up Ret_Ag_Up 10.92340731 3.762356e-212 462
## 34 Estr_Ag_Down Ret_Ag_Up 0.25333064 1.000000e+00 26
## 35 Andr_Ag_Up Ret_Ag_Up 15.73954967 2.013961e-03 4
## 36 Andr_Ag_Down Ret_Ag_Up 0.00000000 1.000000e+00 0
## 37 GC_Ag_Up Ret_Ag_Up 1.57129089 5.128154e-01 1
## 38 GC_Ag_Down Ret_Ag_Up 0.00000000 1.000000e+00 0
## 39 LivX_Ag_Up Ret_Ag_Up 44.20140863 1.730574e-276 367
## 40 LivX_Ag_Down Ret_Ag_Up 0.10123069 1.000000e+00 5
## 41 AhHyd_Ag_Up Ret_Ag_Up 0.00000000 1.000000e+00 0
## 42 AhHyd_Ag_Down Ret_Ag_Up 4.50163038 6.035614e-07 21
## 43 Thyr_Ag_Up Ret_Ag_Down 1.07787369 4.373418e-01 14
## 44 Thyr_Ag_Down Ret_Ag_Down 0.98471188 6.150185e-01 2
## 45 Ret_Ag_Up Ret_Ag_Down 0.00000000 1.000000e+00 0
## 46 Ret_Ag_Down Ret_Ag_Down 1.00000000 1.000000e+00 1369
## 47 Estr_Ag_Up Ret_Ag_Down 0.22200854 1.000000e+00 21
## 48 Estr_Ag_Down Ret_Ag_Down 13.68328533 1.370389e-215 401
## 49 Andr_Ag_Up Ret_Ag_Down 1.97010077 4.403334e-01 1
## 50 Andr_Ag_Down Ret_Ag_Down 3.28369103 3.208514e-01 1
## 51 GC_Ag_Up Ret_Ag_Down 4.92848520 9.920095e-02 2
## 52 GC_Ag_Down Ret_Ag_Down 0.00000000 1.000000e+00 0
## 53 LivX_Ag_Up Ret_Ag_Down 0.15127105 1.000000e+00 7
## 54 LivX_Ag_Down Ret_Ag_Down 13.93497718 6.406226e-118 210
## 55 AhHyd_Ag_Up Ret_Ag_Down 0.00000000 1.000000e+00 0
## 56 AhHyd_Ag_Down Ret_Ag_Down 0.35075826 9.749612e-01 2
## 57 Thyr_Ag_Up Estr_Ag_Up 24.46916321 2.641447e-65 84
## 58 Thyr_Ag_Down Estr_Ag_Up 0.00000000 1.000000e+00 0
## 59 Ret_Ag_Up Estr_Ag_Up 10.92340731 3.762356e-212 462
## 60 Ret_Ag_Down Estr_Ag_Up 0.22200854 1.000000e+00 21
## 61 Estr_Ag_Up Estr_Ag_Up 1.00000000 1.000000e+00 905
## 62 Estr_Ag_Down Estr_Ag_Up 0.00000000 1.000000e+00 0
## 63 Andr_Ag_Up Estr_Ag_Up 30.94356191 1.861609e-04 4
## 64 Andr_Ag_Down Estr_Ag_Up 0.00000000 1.000000e+00 0
## 65 GC_Ag_Up Estr_Ag_Up 3.08367430 3.143162e-01 1
## 66 GC_Ag_Down Estr_Ag_Up 0.00000000 1.000000e+00 0
## 67 LivX_Ag_Up Estr_Ag_Up 18.94632507 1.688829e-149 219
## 68 LivX_Ag_Down Estr_Ag_Up 0.07884643 1.000000e+00 2
## 69 AhHyd_Ag_Up Estr_Ag_Up 0.00000000 1.000000e+00 0
## 70 AhHyd_Ag_Down Estr_Ag_Up 2.84825846 8.022330e-03 9
## 71 Thyr_Ag_Up Estr_Ag_Down 0.12396030 9.996186e-01 1
## 72 Thyr_Ag_Down Estr_Ag_Down 10.16370202 1.083997e-05 8
## 73 Ret_Ag_Up Estr_Ag_Down 0.25333064 1.000000e+00 26
## 74 Ret_Ag_Down Estr_Ag_Down 13.68328533 1.370389e-215 401
## 75 Estr_Ag_Up Estr_Ag_Down 0.00000000 1.000000e+00 0
## 76 Estr_Ag_Down Estr_Ag_Down 1.00000000 1.000000e+00 797
## 77 Andr_Ag_Up Estr_Ag_Down 0.00000000 1.000000e+00 0
## 78 Andr_Ag_Down Estr_Ag_Down 17.66147826 1.605467e-02 2
## 79 GC_Ag_Up Estr_Ag_Down 3.52910210 2.818244e-01 1
## 80 GC_Ag_Down Estr_Ag_Down 8.82361218 1.525330e-01 1
## 81 LivX_Ag_Up Estr_Ag_Down 0.11501425 1.000000e+00 3
## 82 LivX_Ag_Down Estr_Ag_Down 4.38737655 3.359345e-21 72
## 83 AhHyd_Ag_Up Estr_Ag_Down 0.00000000 1.000000e+00 0
## 84 AhHyd_Ag_Down Estr_Ag_Down 3.26370576 3.526989e-03 9
## 85 Thyr_Ag_Up Andr_Ag_Up 533.98796429 4.435963e-10 5
## 86 Thyr_Ag_Down Andr_Ag_Up 0.00000000 1.000000e+00 0
## 87 Ret_Ag_Up Andr_Ag_Up 15.73954967 2.013961e-03 4
## 88 Ret_Ag_Down Andr_Ag_Up 1.97010077 4.403334e-01 1
## 89 Estr_Ag_Up Andr_Ag_Up 30.94356191 1.861609e-04 4
## 90 Estr_Ag_Down Andr_Ag_Up 0.00000000 1.000000e+00 0
## 91 Andr_Ag_Up Andr_Ag_Up 1.00000000 1.000000e+00 6
## 92 Andr_Ag_Down Andr_Ag_Up 0.00000000 1.000000e+00 0
## 93 GC_Ag_Up Andr_Ag_Up 0.00000000 1.000000e+00 0
## 94 GC_Ag_Down Andr_Ag_Up 0.00000000 1.000000e+00 0
## 95 LivX_Ag_Up Andr_Ag_Up 161.91078980 1.462864e-07 5
## 96 LivX_Ag_Down Andr_Ag_Up 0.00000000 1.000000e+00 0
## 97 AhHyd_Ag_Up Andr_Ag_Up 0.00000000 1.000000e+00 0
## 98 AhHyd_Ag_Down Andr_Ag_Up 0.00000000 1.000000e+00 0
## 99 Thyr_Ag_Up Andr_Ag_Down 0.00000000 1.000000e+00 0
## 100 Thyr_Ag_Down Andr_Ag_Down 233.87867212 5.913366e-03 1
## 101 Ret_Ag_Up Andr_Ag_Down 0.00000000 1.000000e+00 0
## 102 Ret_Ag_Down Andr_Ag_Down 3.28369103 3.208514e-01 1
## 103 Estr_Ag_Up Andr_Ag_Down 0.00000000 1.000000e+00 0
## 104 Estr_Ag_Down Andr_Ag_Down 17.66147826 1.605467e-02 2
## 105 Andr_Ag_Up Andr_Ag_Down 0.00000000 1.000000e+00 0
## 106 Andr_Ag_Down Andr_Ag_Down 1.00000000 1.000000e+00 4
## 107 GC_Ag_Up Andr_Ag_Down 0.00000000 1.000000e+00 0
## 108 GC_Ag_Down Andr_Ag_Down 0.00000000 1.000000e+00 0
## 109 LivX_Ag_Up Andr_Ag_Down 0.00000000 1.000000e+00 0
## 110 LivX_Ag_Down Andr_Ag_Down 12.61112374 9.925167e-02 1
## 111 AhHyd_Ag_Up Andr_Ag_Down 0.00000000 1.000000e+00 0
## 112 AhHyd_Ag_Down Andr_Ag_Down 86.10940218 1.553317e-02 1
## 113 Thyr_Ag_Up GC_Ag_Up 0.00000000 1.000000e+00 0
## 114 Thyr_Ag_Down GC_Ag_Up 0.00000000 1.000000e+00 0
## 115 Ret_Ag_Up GC_Ag_Up 1.57129089 5.128154e-01 1
## 116 Ret_Ag_Down GC_Ag_Up 4.92848520 9.920095e-02 2
## 117 Estr_Ag_Up GC_Ag_Up 3.08367430 3.143162e-01 1
## 118 Estr_Ag_Down GC_Ag_Up 3.52910210 2.818244e-01 1
## 119 Andr_Ag_Up GC_Ag_Up 0.00000000 1.000000e+00 0
## 120 Andr_Ag_Down GC_Ag_Up 0.00000000 1.000000e+00 0
## 121 GC_Ag_Up GC_Ag_Up 1.00000000 1.000000e+00 6
## 122 GC_Ag_Down GC_Ag_Up 0.00000000 1.000000e+00 0
## 123 LivX_Ag_Up GC_Ag_Up 0.00000000 1.000000e+00 0
## 124 LivX_Ag_Down GC_Ag_Up 0.00000000 1.000000e+00 0
## 125 AhHyd_Ag_Up GC_Ag_Up 0.00000000 1.000000e+00 0
## 126 AhHyd_Ag_Down GC_Ag_Up 0.00000000 1.000000e+00 0
## 127 Thyr_Ag_Up GC_Ag_Down 0.00000000 1.000000e+00 0
## 128 Thyr_Ag_Down GC_Ag_Down 0.00000000 1.000000e+00 0
## 129 Ret_Ag_Up GC_Ag_Down 0.00000000 1.000000e+00 0
## 130 Ret_Ag_Down GC_Ag_Down 0.00000000 1.000000e+00 0
## 131 Estr_Ag_Up GC_Ag_Down 0.00000000 1.000000e+00 0
## 132 Estr_Ag_Down GC_Ag_Down 8.82361218 1.525330e-01 1
## 133 Andr_Ag_Up GC_Ag_Down 0.00000000 1.000000e+00 0
## 134 Andr_Ag_Down GC_Ag_Down 0.00000000 1.000000e+00 0
## 135 GC_Ag_Up GC_Ag_Down 0.00000000 1.000000e+00 0
## 136 GC_Ag_Down GC_Ag_Down 1.00000000 1.000000e+00 3
## 137 LivX_Ag_Up GC_Ag_Down 0.00000000 1.000000e+00 0
## 138 LivX_Ag_Down GC_Ag_Down 18.91888965 7.540027e-02 1
## 139 AhHyd_Ag_Up GC_Ag_Down 0.00000000 1.000000e+00 0
## 140 AhHyd_Ag_Down GC_Ag_Down 0.00000000 1.000000e+00 0
## 141 Thyr_Ag_Up LivX_Ag_Up 23.63592207 4.556114e-48 56
## 142 Thyr_Ag_Down LivX_Ag_Up 1.52489175 4.920961e-01 1
## 143 Ret_Ag_Up LivX_Ag_Up 44.20140863 1.730574e-276 367
## 144 Ret_Ag_Down LivX_Ag_Up 0.15127105 1.000000e+00 7
## 145 Estr_Ag_Up LivX_Ag_Up 18.94632507 1.688829e-149 219
## 146 Estr_Ag_Down LivX_Ag_Up 0.11501425 1.000000e+00 3
## 147 Andr_Ag_Up LivX_Ag_Up 161.91078981 1.462864e-07 5
## 148 Andr_Ag_Down LivX_Ag_Up 0.00000000 1.000000e+00 0
## 149 GC_Ag_Up LivX_Ag_Up 0.00000000 1.000000e+00 0
## 150 GC_Ag_Down LivX_Ag_Up 0.00000000 1.000000e+00 0
## 151 LivX_Ag_Up LivX_Ag_Up 1.00000000 1.000000e+00 450
## 152 LivX_Ag_Down LivX_Ag_Up 0.00000000 1.000000e+00 0
## 153 AhHyd_Ag_Up LivX_Ag_Up 0.00000000 1.000000e+00 0
## 154 AhHyd_Ag_Down LivX_Ag_Up 3.04112595 3.077775e-02 5
## 155 Thyr_Ag_Up LivX_Ag_Down 0.00000000 1.000000e+00 0
## 156 Thyr_Ag_Down LivX_Ag_Down 0.00000000 1.000000e+00 0
## 157 Ret_Ag_Up LivX_Ag_Down 0.10123069 1.000000e+00 5
## 158 Ret_Ag_Down LivX_Ag_Down 13.93497718 6.406226e-118 210
## 159 Estr_Ag_Up LivX_Ag_Down 0.07884643 1.000000e+00 2
## 160 Estr_Ag_Down LivX_Ag_Down 4.38737655 3.359345e-21 72
## 161 Andr_Ag_Up LivX_Ag_Down 0.00000000 1.000000e+00 0
## 162 Andr_Ag_Down LivX_Ag_Down 12.61112374 9.925167e-02 1
## 163 GC_Ag_Up LivX_Ag_Down 0.00000000 1.000000e+00 0
## 164 GC_Ag_Down LivX_Ag_Down 18.91888965 7.540027e-02 1
## 165 LivX_Ag_Up LivX_Ag_Down 0.00000000 1.000000e+00 0
## 166 LivX_Ag_Down LivX_Ag_Down 1.00000000 1.000000e+00 383
## 167 AhHyd_Ag_Up LivX_Ag_Down 0.00000000 1.000000e+00 0
## 168 AhHyd_Ag_Down LivX_Ag_Down 0.66181252 7.809545e-01 1
## 169 Thyr_Ag_Up AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 170 Thyr_Ag_Down AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 171 Ret_Ag_Up AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 172 Ret_Ag_Down AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 173 Estr_Ag_Up AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 174 Estr_Ag_Down AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 175 Andr_Ag_Up AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 176 Andr_Ag_Down AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 177 GC_Ag_Up AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 178 GC_Ag_Down AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 179 LivX_Ag_Up AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 180 LivX_Ag_Down AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 181 AhHyd_Ag_Up AhHyd_Ag_Up 1.00000000 1.000000e+00 3
## 182 AhHyd_Ag_Down AhHyd_Ag_Up 0.00000000 1.000000e+00 0
## 183 Thyr_Ag_Up AhHyd_Ag_Down 0.00000000 1.000000e+00 0
## 184 Thyr_Ag_Down AhHyd_Ag_Down 380.70756337 2.344408e-24 12
## 185 Ret_Ag_Up AhHyd_Ag_Down 4.50163038 6.035614e-07 21
## 186 Ret_Ag_Down AhHyd_Ag_Down 0.35075826 9.749612e-01 2
## 187 Estr_Ag_Up AhHyd_Ag_Down 2.84825846 8.022330e-03 9
## 188 Estr_Ag_Down AhHyd_Ag_Down 3.26370576 3.526989e-03 9
## 189 Andr_Ag_Up AhHyd_Ag_Down 0.00000000 1.000000e+00 0
## 190 Andr_Ag_Down AhHyd_Ag_Down 86.10940218 1.553317e-02 1
## 191 GC_Ag_Up AhHyd_Ag_Down 0.00000000 1.000000e+00 0
## 192 GC_Ag_Down AhHyd_Ag_Down 0.00000000 1.000000e+00 0
## 193 LivX_Ag_Up AhHyd_Ag_Down 3.04112595 3.077775e-02 5
## 194 LivX_Ag_Down AhHyd_Ag_Down 0.66181252 7.809545e-01 1
## 195 AhHyd_Ag_Up AhHyd_Ag_Down 0.00000000 1.000000e+00 0
## 196 AhHyd_Ag_Down AhHyd_Ag_Down 1.00000000 1.000000e+00 58DotPlot: visualization
I select as significant overlaps having an OR > 2 and at least 25 overlapping genes. Dots are shown for PVals < 0.01 (set in the plot). Max value in the plot must be set according to minimum PVal to avoid dots not to be shown.
cols <- viridis::cividis(100)[1:80]
ResSel <- dplyr::filter(ResMod, OR > 2) %>% dplyr::filter(Numbers > 25)
min(ResSel$Pval)## [1] 1.730574e-276max(ResSel$OR)## [1] 44.20141Dot <- ggplot(ResSel, aes(DEGs, KBase, label=Numbers)) +
geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1)) +
ggtitle('Overlap across agonist-modulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_Agonist.pdf'), width=8, height=8)3.3 Visualize overlap results selectively for retinoic, liverX, estrogen, thyroid
Selection
Path <- c('Thyr_Ag_Up', 'Thyr_Ag_Down', 'Ret_Ag_Up', 'Ret_Ag_Down',
'Estr_Ag_Up', 'Estr_Ag_Down', 'LivX_Ag_Up', 'LivX_Ag_Down')
ResPath <- ResSel[ResSel$DEGs %in% Path & ResSel$KBase %in% Path, ]
ResPath
## DEGs KBase OR Pval Numbers
## 1 Ret_Ag_Up Thyr_Ag_Up 10.905715 3.063677e-40 81
## 2 Estr_Ag_Up Thyr_Ag_Up 24.469163 2.641447e-65 84
## 3 LivX_Ag_Up Thyr_Ag_Up 23.635922 4.556114e-48 56
## 4 Thyr_Ag_Up Ret_Ag_Up 10.905715 3.063677e-40 81
## 5 Estr_Ag_Up Ret_Ag_Up 10.923407 3.762356e-212 462
## 6 LivX_Ag_Up Ret_Ag_Up 44.201409 1.730574e-276 367
## 7 Estr_Ag_Down Ret_Ag_Down 13.683285 1.370389e-215 401
## 8 LivX_Ag_Down Ret_Ag_Down 13.934977 6.406226e-118 210
## 9 Thyr_Ag_Up Estr_Ag_Up 24.469163 2.641447e-65 84
## 10 Ret_Ag_Up Estr_Ag_Up 10.923407 3.762356e-212 462
## 11 LivX_Ag_Up Estr_Ag_Up 18.946325 1.688829e-149 219
## 12 Ret_Ag_Down Estr_Ag_Down 13.683285 1.370389e-215 401
## 13 LivX_Ag_Down Estr_Ag_Down 4.387377 3.359345e-21 72
## 14 Thyr_Ag_Up LivX_Ag_Up 23.635922 4.556114e-48 56
## 15 Ret_Ag_Up LivX_Ag_Up 44.201409 1.730574e-276 367
## 16 Estr_Ag_Up LivX_Ag_Up 18.946325 1.688829e-149 219
## 17 Ret_Ag_Down LivX_Ag_Down 13.934977 6.406226e-118 210
## 18 Estr_Ag_Down LivX_Ag_Down 4.387377 3.359345e-21 72DotPlot: visualization
ResPath <- dplyr::filter(ResPath, OR > 2) %>% dplyr::filter(Numbers > 25)
min(ResPath$Pval)## [1] 1.730574e-276max(ResPath$OR)## [1] 44.20141Dot <- ggplot(ResPath, aes(DEGs, KBase, label=Numbers)) +
geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1))+
ggtitle('Overlap across agonist-modulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_Agonist_Selected.pdf'), width=8, height=8)4. Comparison across pathways: treatment with Inhibitor
4.1 Perform Overlap
DEGs_Inh <- list(
Thyr_Inh_Up= row.names(DEA$Thyr$Inhibitor$DEGs[DEA$Thyr$Inhibitor$DEGs$log2FoldChange > 0, ]),
Thyr_Inh_Down= row.names(DEA$Thyr$Inhibitor$DEGs[DEA$Thyr$Inhibitor$DEGs$log2FoldChange < 0, ]),
Ret_Inh_Up= row.names(DEA$Ret$Inhibitor$DEGs[DEA$Ret$Inhibitor$DEGs$log2FoldChange > 0, ]),
Ret_Inh_Down= row.names(DEA$Ret$Inhibitor$DEGs[DEA$Ret$Inhibitor$DEGs$log2FoldChange < 0, ]),
Andr_Inh_Up= row.names(DEA$Andr$Inhibitor$DEGs[DEA$Andr$Inhibitor$DEGs$log2FoldChange > 0, ]),
Andr_Inh_Down= row.names(DEA$Andr$Inhibitor$DEGs[DEA$Andr$Inhibitor$DEGs$log2FoldChange < 0, ]),
GC_Inh_Up= row.names(DEA$GC$Inhibitor$DEGs[DEA$GC$Inhibitor$DEGs$log2FoldChange > 0, ]),
GC_Inh_Down= row.names(DEA$GC$Inhibitor$DEGs[DEA$GC$Inhibitor$DEGs$log2FoldChange < 0, ]),
LivX_Inh_Up= row.names(DEA$LivX$Inhibitor$DEGs[DEA$LivX$Inhibitor$DEGs$log2FoldChange > 0, ]),
LivX_Inh_Down= row.names(DEA$LivX$Inhibitor$DEGs[DEA$LivX$Inhibitor$DEGs$log2FoldChange < 0, ]),
AhHyd_Inh_Up= row.names(DEA$AhHyd$Inhibitor$DEGs[DEA$AhHyd$Inhibitor$DEGs$log2FoldChange > 0, ]),
AhHyd_Inh_Down= row.names(DEA$AhHyd$Inhibitor$DEGs[DEA$AhHyd$Inhibitor$DEGs$log2FoldChange < 0, ])
)Universe <- row.names(DEA$Ret$Inhibitor$Res) %>% unique()
length(Universe)
## [1] 14850OvObj <- newGOM(DEGs_Inh, DEGs_Inh, genome.size=length(Universe))
print(OvObj)
## A GeneOverlapMatrix object:
## ###### Intersection ######
## Thyr_Inh_Up Thyr_Inh_Down Ret_Inh_Up Ret_Inh_Down Andr_Inh_Up
## Thyr_Inh_Up 270 0 0 2 0
## Thyr_Inh_Down 0 188 0 1 0
## Ret_Inh_Up 0 0 1 0 0
## Ret_Inh_Down 2 1 0 7 0
## Andr_Inh_Up 0 0 0 0 1
## Andr_Inh_Down 3 0 0 1 0
## GC_Inh_Up 19 0 0 1 0
## GC_Inh_Down 0 65 0 1 0
## LivX_Inh_Up 0 0 0 0 0
## LivX_Inh_Down 2 4 0 6 0
## AhHyd_Inh_Up 5 0 1 0 0
## AhHyd_Inh_Down 0 8 0 0 1
## Andr_Inh_Down GC_Inh_Up GC_Inh_Down LivX_Inh_Up LivX_Inh_Down
## Thyr_Inh_Up 3 19 0 0 2
## Thyr_Inh_Down 0 0 65 0 4
## Ret_Inh_Up 0 0 0 0 0
## Ret_Inh_Down 1 1 1 0 6
## Andr_Inh_Up 0 0 0 0 0
## Andr_Inh_Down 8 4 1 0 3
## GC_Inh_Up 4 48 0 0 2
## GC_Inh_Down 1 0 303 0 10
## LivX_Inh_Up 0 0 0 4 0
## LivX_Inh_Down 3 2 10 0 42
## AhHyd_Inh_Up 0 1 1 0 0
## AhHyd_Inh_Down 0 0 3 0 2
## AhHyd_Inh_Up AhHyd_Inh_Down
## Thyr_Inh_Up 5 0
## Thyr_Inh_Down 0 8
## Ret_Inh_Up 1 0
## Ret_Inh_Down 0 0
## Andr_Inh_Up 0 1
## Andr_Inh_Down 0 0
## GC_Inh_Up 1 0
## GC_Inh_Down 1 3
## LivX_Inh_Up 0 0
## LivX_Inh_Down 0 2
## AhHyd_Inh_Up 13 0
## AhHyd_Inh_Down 0 29
## ###### P-value ######
## Thyr_Inh_Up Thyr_Inh_Down Ret_Inh_Up Ret_Inh_Down
## Thyr_Inh_Up 0.000000e+00 1.000000e+00 1.000000e+00 6.511812e-03
## Thyr_Inh_Down 1.000000e+00 0.000000e+00 1.000000e+00 8.534049e-02
## Ret_Inh_Up 1.000000e+00 1.000000e+00 6.734007e-05 1.000000e+00
## Ret_Inh_Down 6.511812e-03 8.534049e-02 1.000000e+00 3.169273e-26
## Andr_Inh_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## Andr_Inh_Down 3.111080e-04 1.000000e+00 1.000000e+00 3.765714e-03
## GC_Inh_Up 3.270578e-21 1.000000e+00 1.000000e+00 2.241252e-02
## GC_Inh_Down 1.000000e+00 3.521227e-63 1.000000e+00 1.344023e-01
## LivX_Inh_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## LivX_Inh_Down 1.772825e-01 1.912469e-03 1.000000e+00 2.462733e-15
## AhHyd_Inh_Up 2.187153e-06 1.000000e+00 8.754209e-04 1.000000e+00
## AhHyd_Inh_Down 1.000000e+00 1.943615e-09 1.000000e+00 1.000000e+00
## Andr_Inh_Up Andr_Inh_Down GC_Inh_Up GC_Inh_Down
## Thyr_Inh_Up 1.000000e+00 3.111080e-04 3.270578e-21 1.000000e+00
## Thyr_Inh_Down 1.000000e+00 1.000000e+00 1.000000e+00 3.521227e-63
## Ret_Inh_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## Ret_Inh_Down 1.000000e+00 3.765714e-03 2.241252e-02 1.344023e-01
## Andr_Inh_Up 6.734007e-05 1.000000e+00 1.000000e+00 1.000000e+00
## Andr_Inh_Down 1.000000e+00 1.708157e-29 6.661218e-09 1.520723e-01
## GC_Inh_Up 1.000000e+00 6.661218e-09 7.657078e-140 1.000000e+00
## GC_Inh_Down 1.000000e+00 1.520723e-01 1.000000e+00 0.000000e+00
## LivX_Inh_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## LivX_Inh_Down 1.000000e+00 1.166562e-06 8.112407e-03 8.906368e-09
## AhHyd_Inh_Up 1.000000e+00 1.000000e+00 4.123119e-02 2.351729e-01
## AhHyd_Inh_Down 1.952862e-03 1.000000e+00 1.000000e+00 2.077014e-02
## LivX_Inh_Up LivX_Inh_Down AhHyd_Inh_Up AhHyd_Inh_Down
## Thyr_Inh_Up 1.000000e+00 1.772825e-01 2.187153e-06 1.000000e+00
## Thyr_Inh_Down 1.000000e+00 1.912469e-03 1.000000e+00 1.943615e-09
## Ret_Inh_Up 1.000000e+00 1.000000e+00 8.754209e-04 1.000000e+00
## Ret_Inh_Down 1.000000e+00 2.462733e-15 1.000000e+00 1.000000e+00
## Andr_Inh_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.952862e-03
## Andr_Inh_Down 1.000000e+00 1.166562e-06 1.000000e+00 1.000000e+00
## GC_Inh_Up 1.000000e+00 8.112407e-03 4.123119e-02 1.000000e+00
## GC_Inh_Down 1.000000e+00 8.906368e-09 2.351729e-01 2.077014e-02
## LivX_Inh_Up 4.937202e-16 1.000000e+00 1.000000e+00 1.000000e+00
## LivX_Inh_Down 1.000000e+00 9.127902e-125 1.000000e+00 3.020683e-03
## AhHyd_Inh_Up 1.000000e+00 1.000000e+00 3.665373e-45 1.000000e+00
## AhHyd_Inh_Down 1.000000e+00 3.020683e-03 1.000000e+00 9.513776e-91
## ###### Odds Ratio ######
## Thyr_Inh_Up Thyr_Inh_Down Ret_Inh_Up Ret_Inh_Down Andr_Inh_Up
## Thyr_Inh_Up Inf 0.000000 0 21.730217 0
## Thyr_Inh_Down 0.000000 Inf 0 13.053133 0
## Ret_Inh_Up 0.000000 0.000000 Inf 0.000000 0
## Ret_Inh_Down 21.730217 13.053133 0 Inf 0
## Andr_Inh_Up 0.000000 0.000000 0 0.000000 Inf
## Andr_Inh_Down 32.708898 0.000000 0 347.875457 0
## GC_Inh_Up 37.929142 0.000000 0 52.274907 0
## GC_Inh_Down 0.000000 31.989423 0 8.021994 0
## LivX_Inh_Up 0.000000 0.000000 0 0.000000 0
## LivX_Inh_Down 2.712281 8.362407 0 2421.329155 0
## AhHyd_Inh_Up 34.320883 0.000000 Inf 0.000000 0
## AhHyd_Inh_Down 0.000000 30.931807 0 0.000000 Inf
## Andr_Inh_Down GC_Inh_Up GC_Inh_Down LivX_Inh_Up LivX_Inh_Down
## Thyr_Inh_Up 32.708898 37.92914 0.000000 0 2.712281
## Thyr_Inh_Down 0.000000 0.00000 31.989423 0 8.362407
## Ret_Inh_Up 0.000000 0.00000 0.000000 0 0.000000
## Ret_Inh_Down 347.875457 52.27491 8.021994 0 2421.329155
## Andr_Inh_Up 0.000000 0.00000 0.000000 0 0.000000
## Andr_Inh_Down Inf 333.44051 6.875475 0 224.966301
## GC_Inh_Up 333.440509 Inf 0.000000 0 16.030728
## GC_Inh_Down 6.875475 0.00000 Inf 0 15.473027
## LivX_Inh_Up 0.000000 0.00000 0.000000 Inf 0.000000
## LivX_Inh_Down 224.966301 16.03073 15.473027 0 Inf
## AhHyd_Inh_Up 0.000000 26.19770 4.010017 0 0.000000
## AhHyd_Inh_Down 0.000000 0.00000 5.583418 0 27.338048
## AhHyd_Inh_Up AhHyd_Inh_Down
## Thyr_Inh_Up 34.320883 0.000000
## Thyr_Inh_Down 0.000000 30.931807
## Ret_Inh_Up Inf 0.000000
## Ret_Inh_Down 0.000000 0.000000
## Andr_Inh_Up 0.000000 Inf
## Andr_Inh_Down 0.000000 0.000000
## GC_Inh_Up 26.197703 0.000000
## GC_Inh_Down 4.010017 5.583418
## LivX_Inh_Up 0.000000 0.000000
## LivX_Inh_Down 0.000000 27.338048
## AhHyd_Inh_Up Inf 0.000000
## AhHyd_Inh_Down 0.000000 Inf
## ###### Jaccard Index ######
## Thyr_Inh_Up Thyr_Inh_Down Ret_Inh_Up Ret_Inh_Down Andr_Inh_Up
## Thyr_Inh_Up 1.000000000 0.000000000 0.00000000 0.007272727 0.00000000
## Thyr_Inh_Down 0.000000000 1.000000000 0.00000000 0.005154639 0.00000000
## Ret_Inh_Up 0.000000000 0.000000000 1.00000000 0.000000000 0.00000000
## Ret_Inh_Down 0.007272727 0.005154639 0.00000000 1.000000000 0.00000000
## Andr_Inh_Up 0.000000000 0.000000000 0.00000000 0.000000000 1.00000000
## Andr_Inh_Down 0.010909091 0.000000000 0.00000000 0.071428571 0.00000000
## GC_Inh_Up 0.063545151 0.000000000 0.00000000 0.018518519 0.00000000
## GC_Inh_Down 0.000000000 0.152582160 0.00000000 0.003236246 0.00000000
## LivX_Inh_Up 0.000000000 0.000000000 0.00000000 0.000000000 0.00000000
## LivX_Inh_Down 0.006451613 0.017699115 0.00000000 0.139534884 0.00000000
## AhHyd_Inh_Up 0.017985612 0.000000000 0.07692308 0.000000000 0.00000000
## AhHyd_Inh_Down 0.000000000 0.038277512 0.00000000 0.000000000 0.03448276
## Andr_Inh_Down GC_Inh_Up GC_Inh_Down LivX_Inh_Up LivX_Inh_Down
## Thyr_Inh_Up 0.010909091 0.06354515 0.000000000 0 0.006451613
## Thyr_Inh_Down 0.000000000 0.00000000 0.152582160 0 0.017699115
## Ret_Inh_Up 0.000000000 0.00000000 0.000000000 0 0.000000000
## Ret_Inh_Down 0.071428571 0.01851852 0.003236246 0 0.139534884
## Andr_Inh_Up 0.000000000 0.00000000 0.000000000 0 0.000000000
## Andr_Inh_Down 1.000000000 0.07692308 0.003225806 0 0.063829787
## GC_Inh_Up 0.076923077 1.00000000 0.000000000 0 0.022727273
## GC_Inh_Down 0.003225806 0.00000000 1.000000000 0 0.029850746
## LivX_Inh_Up 0.000000000 0.00000000 0.000000000 1 0.000000000
## LivX_Inh_Down 0.063829787 0.02272727 0.029850746 0 1.000000000
## AhHyd_Inh_Up 0.000000000 0.01666667 0.003174603 0 0.000000000
## AhHyd_Inh_Down 0.000000000 0.00000000 0.009118541 0 0.028985507
## AhHyd_Inh_Up AhHyd_Inh_Down
## Thyr_Inh_Up 0.017985612 0.000000000
## Thyr_Inh_Down 0.000000000 0.038277512
## Ret_Inh_Up 0.076923077 0.000000000
## Ret_Inh_Down 0.000000000 0.000000000
## Andr_Inh_Up 0.000000000 0.034482759
## Andr_Inh_Down 0.000000000 0.000000000
## GC_Inh_Up 0.016666667 0.000000000
## GC_Inh_Down 0.003174603 0.009118541
## LivX_Inh_Up 0.000000000 0.000000000
## LivX_Inh_Down 0.000000000 0.028985507
## AhHyd_Inh_Up 1.000000000 0.000000000
## AhHyd_Inh_Down 0.000000000 1.000000000getMatrix(OvObj, name='intersection')
## Thyr_Inh_Up Thyr_Inh_Down Ret_Inh_Up Ret_Inh_Down Andr_Inh_Up
## Thyr_Inh_Up 270 0 0 2 0
## Thyr_Inh_Down 0 188 0 1 0
## Ret_Inh_Up 0 0 1 0 0
## Ret_Inh_Down 2 1 0 7 0
## Andr_Inh_Up 0 0 0 0 1
## Andr_Inh_Down 3 0 0 1 0
## GC_Inh_Up 19 0 0 1 0
## GC_Inh_Down 0 65 0 1 0
## LivX_Inh_Up 0 0 0 0 0
## LivX_Inh_Down 2 4 0 6 0
## AhHyd_Inh_Up 5 0 1 0 0
## AhHyd_Inh_Down 0 8 0 0 1
## Andr_Inh_Down GC_Inh_Up GC_Inh_Down LivX_Inh_Up LivX_Inh_Down
## Thyr_Inh_Up 3 19 0 0 2
## Thyr_Inh_Down 0 0 65 0 4
## Ret_Inh_Up 0 0 0 0 0
## Ret_Inh_Down 1 1 1 0 6
## Andr_Inh_Up 0 0 0 0 0
## Andr_Inh_Down 8 4 1 0 3
## GC_Inh_Up 4 48 0 0 2
## GC_Inh_Down 1 0 303 0 10
## LivX_Inh_Up 0 0 0 4 0
## LivX_Inh_Down 3 2 10 0 42
## AhHyd_Inh_Up 0 1 1 0 0
## AhHyd_Inh_Down 0 0 3 0 2
## AhHyd_Inh_Up AhHyd_Inh_Down
## Thyr_Inh_Up 5 0
## Thyr_Inh_Down 0 8
## Ret_Inh_Up 1 0
## Ret_Inh_Down 0 0
## Andr_Inh_Up 0 1
## Andr_Inh_Down 0 0
## GC_Inh_Up 1 0
## GC_Inh_Down 1 3
## LivX_Inh_Up 0 0
## LivX_Inh_Down 0 2
## AhHyd_Inh_Up 13 0
## AhHyd_Inh_Down 0 29getMatrix(OvObj, name='pval')
## Thyr_Inh_Up Thyr_Inh_Down Ret_Inh_Up Ret_Inh_Down
## Thyr_Inh_Up 0.000000e+00 1.000000e+00 1.000000e+00 6.511812e-03
## Thyr_Inh_Down 1.000000e+00 0.000000e+00 1.000000e+00 8.534049e-02
## Ret_Inh_Up 1.000000e+00 1.000000e+00 6.734007e-05 1.000000e+00
## Ret_Inh_Down 6.511812e-03 8.534049e-02 1.000000e+00 3.169273e-26
## Andr_Inh_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## Andr_Inh_Down 3.111080e-04 1.000000e+00 1.000000e+00 3.765714e-03
## GC_Inh_Up 3.270578e-21 1.000000e+00 1.000000e+00 2.241252e-02
## GC_Inh_Down 1.000000e+00 3.521227e-63 1.000000e+00 1.344023e-01
## LivX_Inh_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## LivX_Inh_Down 1.772825e-01 1.912469e-03 1.000000e+00 2.462733e-15
## AhHyd_Inh_Up 2.187153e-06 1.000000e+00 8.754209e-04 1.000000e+00
## AhHyd_Inh_Down 1.000000e+00 1.943615e-09 1.000000e+00 1.000000e+00
## Andr_Inh_Up Andr_Inh_Down GC_Inh_Up GC_Inh_Down
## Thyr_Inh_Up 1.000000e+00 3.111080e-04 3.270578e-21 1.000000e+00
## Thyr_Inh_Down 1.000000e+00 1.000000e+00 1.000000e+00 3.521227e-63
## Ret_Inh_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## Ret_Inh_Down 1.000000e+00 3.765714e-03 2.241252e-02 1.344023e-01
## Andr_Inh_Up 6.734007e-05 1.000000e+00 1.000000e+00 1.000000e+00
## Andr_Inh_Down 1.000000e+00 1.708157e-29 6.661218e-09 1.520723e-01
## GC_Inh_Up 1.000000e+00 6.661218e-09 7.657078e-140 1.000000e+00
## GC_Inh_Down 1.000000e+00 1.520723e-01 1.000000e+00 0.000000e+00
## LivX_Inh_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## LivX_Inh_Down 1.000000e+00 1.166562e-06 8.112407e-03 8.906368e-09
## AhHyd_Inh_Up 1.000000e+00 1.000000e+00 4.123119e-02 2.351729e-01
## AhHyd_Inh_Down 1.952862e-03 1.000000e+00 1.000000e+00 2.077014e-02
## LivX_Inh_Up LivX_Inh_Down AhHyd_Inh_Up AhHyd_Inh_Down
## Thyr_Inh_Up 1.000000e+00 1.772825e-01 2.187153e-06 1.000000e+00
## Thyr_Inh_Down 1.000000e+00 1.912469e-03 1.000000e+00 1.943615e-09
## Ret_Inh_Up 1.000000e+00 1.000000e+00 8.754209e-04 1.000000e+00
## Ret_Inh_Down 1.000000e+00 2.462733e-15 1.000000e+00 1.000000e+00
## Andr_Inh_Up 1.000000e+00 1.000000e+00 1.000000e+00 1.952862e-03
## Andr_Inh_Down 1.000000e+00 1.166562e-06 1.000000e+00 1.000000e+00
## GC_Inh_Up 1.000000e+00 8.112407e-03 4.123119e-02 1.000000e+00
## GC_Inh_Down 1.000000e+00 8.906368e-09 2.351729e-01 2.077014e-02
## LivX_Inh_Up 4.937202e-16 1.000000e+00 1.000000e+00 1.000000e+00
## LivX_Inh_Down 1.000000e+00 9.127902e-125 1.000000e+00 3.020683e-03
## AhHyd_Inh_Up 1.000000e+00 1.000000e+00 3.665373e-45 1.000000e+00
## AhHyd_Inh_Down 1.000000e+00 3.020683e-03 1.000000e+00 9.513776e-91getMatrix(OvObj, name='odds.ratio')
## Thyr_Inh_Up Thyr_Inh_Down Ret_Inh_Up Ret_Inh_Down Andr_Inh_Up
## Thyr_Inh_Up Inf 0.000000 0 21.730217 0
## Thyr_Inh_Down 0.000000 Inf 0 13.053133 0
## Ret_Inh_Up 0.000000 0.000000 Inf 0.000000 0
## Ret_Inh_Down 21.730217 13.053133 0 Inf 0
## Andr_Inh_Up 0.000000 0.000000 0 0.000000 Inf
## Andr_Inh_Down 32.708898 0.000000 0 347.875457 0
## GC_Inh_Up 37.929142 0.000000 0 52.274907 0
## GC_Inh_Down 0.000000 31.989423 0 8.021994 0
## LivX_Inh_Up 0.000000 0.000000 0 0.000000 0
## LivX_Inh_Down 2.712281 8.362407 0 2421.329155 0
## AhHyd_Inh_Up 34.320883 0.000000 Inf 0.000000 0
## AhHyd_Inh_Down 0.000000 30.931807 0 0.000000 Inf
## Andr_Inh_Down GC_Inh_Up GC_Inh_Down LivX_Inh_Up LivX_Inh_Down
## Thyr_Inh_Up 32.708898 37.92914 0.000000 0 2.712281
## Thyr_Inh_Down 0.000000 0.00000 31.989423 0 8.362407
## Ret_Inh_Up 0.000000 0.00000 0.000000 0 0.000000
## Ret_Inh_Down 347.875457 52.27491 8.021994 0 2421.329155
## Andr_Inh_Up 0.000000 0.00000 0.000000 0 0.000000
## Andr_Inh_Down Inf 333.44051 6.875475 0 224.966301
## GC_Inh_Up 333.440509 Inf 0.000000 0 16.030728
## GC_Inh_Down 6.875475 0.00000 Inf 0 15.473027
## LivX_Inh_Up 0.000000 0.00000 0.000000 Inf 0.000000
## LivX_Inh_Down 224.966301 16.03073 15.473027 0 Inf
## AhHyd_Inh_Up 0.000000 26.19770 4.010017 0 0.000000
## AhHyd_Inh_Down 0.000000 0.00000 5.583418 0 27.338048
## AhHyd_Inh_Up AhHyd_Inh_Down
## Thyr_Inh_Up 34.320883 0.000000
## Thyr_Inh_Down 0.000000 30.931807
## Ret_Inh_Up Inf 0.000000
## Ret_Inh_Down 0.000000 0.000000
## Andr_Inh_Up 0.000000 Inf
## Andr_Inh_Down 0.000000 0.000000
## GC_Inh_Up 26.197703 0.000000
## GC_Inh_Down 4.010017 5.583418
## LivX_Inh_Up 0.000000 0.000000
## LivX_Inh_Down 0.000000 27.338048
## AhHyd_Inh_Up Inf 0.000000
## AhHyd_Inh_Down 0.000000 Inf4.2 Visualize overlap results
DotPlot: data preparation
OR <- data.frame(getMatrix(OvObj, name='odds.ratio'))
OR$DEGs <- row.names(OR)
OR <- gather(OR, 'KBase', 'OR', -DEGs)
PVAL <- data.frame(getMatrix(OvObj, name='pval'))
PVAL$DEGs <- row.names(PVAL)
PVAL <- gather(PVAL, 'KBase', 'PVal', -DEGs)
NUM <- data.frame(getMatrix(OvObj, name='intersection'))
NUM$DEGs <- row.names(NUM)
NUM <- gather(NUM, 'KBase', 'Numbers', -DEGs)
if(! identical(OR$DEGs, PVAL$DEGs)){
stop('Inconsistecy')
}
if(! identical(OR$DEGs, NUM$DEGs)){
stop('Inconsistecy')
}
if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}
if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}
Res <- mutate(OR, Pval=PVAL$PVal) %>% mutate(Numbers=NUM$Numbers)
Res
## DEGs KBase OR Pval Numbers
## 1 Thyr_Inh_Up Thyr_Inh_Up Inf 0.000000e+00 270
## 2 Thyr_Inh_Down Thyr_Inh_Up 0.000000 1.000000e+00 0
## 3 Ret_Inh_Up Thyr_Inh_Up 0.000000 1.000000e+00 0
## 4 Ret_Inh_Down Thyr_Inh_Up 21.730217 6.511812e-03 2
## 5 Andr_Inh_Up Thyr_Inh_Up 0.000000 1.000000e+00 0
## 6 Andr_Inh_Down Thyr_Inh_Up 32.708898 3.111080e-04 3
## 7 GC_Inh_Up Thyr_Inh_Up 37.929142 3.270578e-21 19
## 8 GC_Inh_Down Thyr_Inh_Up 0.000000 1.000000e+00 0
## 9 LivX_Inh_Up Thyr_Inh_Up 0.000000 1.000000e+00 0
## 10 LivX_Inh_Down Thyr_Inh_Up 2.712281 1.772825e-01 2
## 11 AhHyd_Inh_Up Thyr_Inh_Up 34.320883 2.187153e-06 5
## 12 AhHyd_Inh_Down Thyr_Inh_Up 0.000000 1.000000e+00 0
## 13 Thyr_Inh_Up Thyr_Inh_Down 0.000000 1.000000e+00 0
## 14 Thyr_Inh_Down Thyr_Inh_Down Inf 0.000000e+00 188
## 15 Ret_Inh_Up Thyr_Inh_Down 0.000000 1.000000e+00 0
## 16 Ret_Inh_Down Thyr_Inh_Down 13.053133 8.534049e-02 1
## 17 Andr_Inh_Up Thyr_Inh_Down 0.000000 1.000000e+00 0
## 18 Andr_Inh_Down Thyr_Inh_Down 0.000000 1.000000e+00 0
## 19 GC_Inh_Up Thyr_Inh_Down 0.000000 1.000000e+00 0
## 20 GC_Inh_Down Thyr_Inh_Down 31.989423 3.521227e-63 65
## 21 LivX_Inh_Up Thyr_Inh_Down 0.000000 1.000000e+00 0
## 22 LivX_Inh_Down Thyr_Inh_Down 8.362407 1.912469e-03 4
## 23 AhHyd_Inh_Up Thyr_Inh_Down 0.000000 1.000000e+00 0
## 24 AhHyd_Inh_Down Thyr_Inh_Down 30.931807 1.943615e-09 8
## 25 Thyr_Inh_Up Ret_Inh_Up 0.000000 1.000000e+00 0
## 26 Thyr_Inh_Down Ret_Inh_Up 0.000000 1.000000e+00 0
## 27 Ret_Inh_Up Ret_Inh_Up Inf 6.734007e-05 1
## 28 Ret_Inh_Down Ret_Inh_Up 0.000000 1.000000e+00 0
## 29 Andr_Inh_Up Ret_Inh_Up 0.000000 1.000000e+00 0
## 30 Andr_Inh_Down Ret_Inh_Up 0.000000 1.000000e+00 0
## 31 GC_Inh_Up Ret_Inh_Up 0.000000 1.000000e+00 0
## 32 GC_Inh_Down Ret_Inh_Up 0.000000 1.000000e+00 0
## 33 LivX_Inh_Up Ret_Inh_Up 0.000000 1.000000e+00 0
## 34 LivX_Inh_Down Ret_Inh_Up 0.000000 1.000000e+00 0
## 35 AhHyd_Inh_Up Ret_Inh_Up Inf 8.754209e-04 1
## 36 AhHyd_Inh_Down Ret_Inh_Up 0.000000 1.000000e+00 0
## 37 Thyr_Inh_Up Ret_Inh_Down 21.730217 6.511812e-03 2
## 38 Thyr_Inh_Down Ret_Inh_Down 13.053133 8.534049e-02 1
## 39 Ret_Inh_Up Ret_Inh_Down 0.000000 1.000000e+00 0
## 40 Ret_Inh_Down Ret_Inh_Down Inf 3.169273e-26 7
## 41 Andr_Inh_Up Ret_Inh_Down 0.000000 1.000000e+00 0
## 42 Andr_Inh_Down Ret_Inh_Down 347.875457 3.765714e-03 1
## 43 GC_Inh_Up Ret_Inh_Down 52.274907 2.241252e-02 1
## 44 GC_Inh_Down Ret_Inh_Down 8.021994 1.344023e-01 1
## 45 LivX_Inh_Up Ret_Inh_Down 0.000000 1.000000e+00 0
## 46 LivX_Inh_Down Ret_Inh_Down 2421.329155 2.462733e-15 6
## 47 AhHyd_Inh_Up Ret_Inh_Down 0.000000 1.000000e+00 0
## 48 AhHyd_Inh_Down Ret_Inh_Down 0.000000 1.000000e+00 0
## 49 Thyr_Inh_Up Andr_Inh_Up 0.000000 1.000000e+00 0
## 50 Thyr_Inh_Down Andr_Inh_Up 0.000000 1.000000e+00 0
## 51 Ret_Inh_Up Andr_Inh_Up 0.000000 1.000000e+00 0
## 52 Ret_Inh_Down Andr_Inh_Up 0.000000 1.000000e+00 0
## 53 Andr_Inh_Up Andr_Inh_Up Inf 6.734007e-05 1
## 54 Andr_Inh_Down Andr_Inh_Up 0.000000 1.000000e+00 0
## 55 GC_Inh_Up Andr_Inh_Up 0.000000 1.000000e+00 0
## 56 GC_Inh_Down Andr_Inh_Up 0.000000 1.000000e+00 0
## 57 LivX_Inh_Up Andr_Inh_Up 0.000000 1.000000e+00 0
## 58 LivX_Inh_Down Andr_Inh_Up 0.000000 1.000000e+00 0
## 59 AhHyd_Inh_Up Andr_Inh_Up 0.000000 1.000000e+00 0
## 60 AhHyd_Inh_Down Andr_Inh_Up Inf 1.952862e-03 1
## 61 Thyr_Inh_Up Andr_Inh_Down 32.708898 3.111080e-04 3
## 62 Thyr_Inh_Down Andr_Inh_Down 0.000000 1.000000e+00 0
## 63 Ret_Inh_Up Andr_Inh_Down 0.000000 1.000000e+00 0
## 64 Ret_Inh_Down Andr_Inh_Down 347.875457 3.765714e-03 1
## 65 Andr_Inh_Up Andr_Inh_Down 0.000000 1.000000e+00 0
## 66 Andr_Inh_Down Andr_Inh_Down Inf 1.708157e-29 8
## 67 GC_Inh_Up Andr_Inh_Down 333.440509 6.661218e-09 4
## 68 GC_Inh_Down Andr_Inh_Down 6.875475 1.520723e-01 1
## 69 LivX_Inh_Up Andr_Inh_Down 0.000000 1.000000e+00 0
## 70 LivX_Inh_Down Andr_Inh_Down 224.966301 1.166562e-06 3
## 71 AhHyd_Inh_Up Andr_Inh_Down 0.000000 1.000000e+00 0
## 72 AhHyd_Inh_Down Andr_Inh_Down 0.000000 1.000000e+00 0
## 73 Thyr_Inh_Up GC_Inh_Up 37.929142 3.270578e-21 19
## 74 Thyr_Inh_Down GC_Inh_Up 0.000000 1.000000e+00 0
## 75 Ret_Inh_Up GC_Inh_Up 0.000000 1.000000e+00 0
## 76 Ret_Inh_Down GC_Inh_Up 52.274907 2.241252e-02 1
## 77 Andr_Inh_Up GC_Inh_Up 0.000000 1.000000e+00 0
## 78 Andr_Inh_Down GC_Inh_Up 333.440509 6.661218e-09 4
## 79 GC_Inh_Up GC_Inh_Up Inf 7.657078e-140 48
## 80 GC_Inh_Down GC_Inh_Up 0.000000 1.000000e+00 0
## 81 LivX_Inh_Up GC_Inh_Up 0.000000 1.000000e+00 0
## 82 LivX_Inh_Down GC_Inh_Up 16.030728 8.112407e-03 2
## 83 AhHyd_Inh_Up GC_Inh_Up 26.197703 4.123119e-02 1
## 84 AhHyd_Inh_Down GC_Inh_Up 0.000000 1.000000e+00 0
## 85 Thyr_Inh_Up GC_Inh_Down 0.000000 1.000000e+00 0
## 86 Thyr_Inh_Down GC_Inh_Down 31.989423 3.521227e-63 65
## 87 Ret_Inh_Up GC_Inh_Down 0.000000 1.000000e+00 0
## 88 Ret_Inh_Down GC_Inh_Down 8.021994 1.344023e-01 1
## 89 Andr_Inh_Up GC_Inh_Down 0.000000 1.000000e+00 0
## 90 Andr_Inh_Down GC_Inh_Down 6.875475 1.520723e-01 1
## 91 GC_Inh_Up GC_Inh_Down 0.000000 1.000000e+00 0
## 92 GC_Inh_Down GC_Inh_Down Inf 0.000000e+00 303
## 93 LivX_Inh_Up GC_Inh_Down 0.000000 1.000000e+00 0
## 94 LivX_Inh_Down GC_Inh_Down 15.473027 8.906368e-09 10
## 95 AhHyd_Inh_Up GC_Inh_Down 4.010017 2.351729e-01 1
## 96 AhHyd_Inh_Down GC_Inh_Down 5.583418 2.077014e-02 3
## 97 Thyr_Inh_Up LivX_Inh_Up 0.000000 1.000000e+00 0
## 98 Thyr_Inh_Down LivX_Inh_Up 0.000000 1.000000e+00 0
## 99 Ret_Inh_Up LivX_Inh_Up 0.000000 1.000000e+00 0
## 100 Ret_Inh_Down LivX_Inh_Up 0.000000 1.000000e+00 0
## 101 Andr_Inh_Up LivX_Inh_Up 0.000000 1.000000e+00 0
## 102 Andr_Inh_Down LivX_Inh_Up 0.000000 1.000000e+00 0
## 103 GC_Inh_Up LivX_Inh_Up 0.000000 1.000000e+00 0
## 104 GC_Inh_Down LivX_Inh_Up 0.000000 1.000000e+00 0
## 105 LivX_Inh_Up LivX_Inh_Up Inf 4.937202e-16 4
## 106 LivX_Inh_Down LivX_Inh_Up 0.000000 1.000000e+00 0
## 107 AhHyd_Inh_Up LivX_Inh_Up 0.000000 1.000000e+00 0
## 108 AhHyd_Inh_Down LivX_Inh_Up 0.000000 1.000000e+00 0
## 109 Thyr_Inh_Up LivX_Inh_Down 2.712281 1.772825e-01 2
## 110 Thyr_Inh_Down LivX_Inh_Down 8.362407 1.912469e-03 4
## 111 Ret_Inh_Up LivX_Inh_Down 0.000000 1.000000e+00 0
## 112 Ret_Inh_Down LivX_Inh_Down 2421.329155 2.462733e-15 6
## 113 Andr_Inh_Up LivX_Inh_Down 0.000000 1.000000e+00 0
## 114 Andr_Inh_Down LivX_Inh_Down 224.966301 1.166562e-06 3
## 115 GC_Inh_Up LivX_Inh_Down 16.030728 8.112407e-03 2
## 116 GC_Inh_Down LivX_Inh_Down 15.473027 8.906368e-09 10
## 117 LivX_Inh_Up LivX_Inh_Down 0.000000 1.000000e+00 0
## 118 LivX_Inh_Down LivX_Inh_Down Inf 9.127902e-125 42
## 119 AhHyd_Inh_Up LivX_Inh_Down 0.000000 1.000000e+00 0
## 120 AhHyd_Inh_Down LivX_Inh_Down 27.338048 3.020683e-03 2
## 121 Thyr_Inh_Up AhHyd_Inh_Up 34.320883 2.187153e-06 5
## 122 Thyr_Inh_Down AhHyd_Inh_Up 0.000000 1.000000e+00 0
## 123 Ret_Inh_Up AhHyd_Inh_Up Inf 8.754209e-04 1
## 124 Ret_Inh_Down AhHyd_Inh_Up 0.000000 1.000000e+00 0
## 125 Andr_Inh_Up AhHyd_Inh_Up 0.000000 1.000000e+00 0
## 126 Andr_Inh_Down AhHyd_Inh_Up 0.000000 1.000000e+00 0
## 127 GC_Inh_Up AhHyd_Inh_Up 26.197703 4.123119e-02 1
## 128 GC_Inh_Down AhHyd_Inh_Up 4.010017 2.351729e-01 1
## 129 LivX_Inh_Up AhHyd_Inh_Up 0.000000 1.000000e+00 0
## 130 LivX_Inh_Down AhHyd_Inh_Up 0.000000 1.000000e+00 0
## 131 AhHyd_Inh_Up AhHyd_Inh_Up Inf 3.665373e-45 13
## 132 AhHyd_Inh_Down AhHyd_Inh_Up 0.000000 1.000000e+00 0
## 133 Thyr_Inh_Up AhHyd_Inh_Down 0.000000 1.000000e+00 0
## 134 Thyr_Inh_Down AhHyd_Inh_Down 30.931807 1.943615e-09 8
## 135 Ret_Inh_Up AhHyd_Inh_Down 0.000000 1.000000e+00 0
## 136 Ret_Inh_Down AhHyd_Inh_Down 0.000000 1.000000e+00 0
## 137 Andr_Inh_Up AhHyd_Inh_Down Inf 1.952862e-03 1
## 138 Andr_Inh_Down AhHyd_Inh_Down 0.000000 1.000000e+00 0
## 139 GC_Inh_Up AhHyd_Inh_Down 0.000000 1.000000e+00 0
## 140 GC_Inh_Down AhHyd_Inh_Down 5.583418 2.077014e-02 3
## 141 LivX_Inh_Up AhHyd_Inh_Down 0.000000 1.000000e+00 0
## 142 LivX_Inh_Down AhHyd_Inh_Down 27.338048 3.020683e-03 2
## 143 AhHyd_Inh_Up AhHyd_Inh_Down 0.000000 1.000000e+00 0
## 144 AhHyd_Inh_Down AhHyd_Inh_Down Inf 9.513776e-91 29ResMod <- Res
ResMod[ResMod$DEGs == ResMod$KBase, ]$OR <- 1
ResMod[ResMod$DEGs == ResMod$KBase, ]$Pval <- 1
ResMod
## DEGs KBase OR Pval Numbers
## 1 Thyr_Inh_Up Thyr_Inh_Up 1.000000 1.000000e+00 270
## 2 Thyr_Inh_Down Thyr_Inh_Up 0.000000 1.000000e+00 0
## 3 Ret_Inh_Up Thyr_Inh_Up 0.000000 1.000000e+00 0
## 4 Ret_Inh_Down Thyr_Inh_Up 21.730217 6.511812e-03 2
## 5 Andr_Inh_Up Thyr_Inh_Up 0.000000 1.000000e+00 0
## 6 Andr_Inh_Down Thyr_Inh_Up 32.708898 3.111080e-04 3
## 7 GC_Inh_Up Thyr_Inh_Up 37.929142 3.270578e-21 19
## 8 GC_Inh_Down Thyr_Inh_Up 0.000000 1.000000e+00 0
## 9 LivX_Inh_Up Thyr_Inh_Up 0.000000 1.000000e+00 0
## 10 LivX_Inh_Down Thyr_Inh_Up 2.712281 1.772825e-01 2
## 11 AhHyd_Inh_Up Thyr_Inh_Up 34.320883 2.187153e-06 5
## 12 AhHyd_Inh_Down Thyr_Inh_Up 0.000000 1.000000e+00 0
## 13 Thyr_Inh_Up Thyr_Inh_Down 0.000000 1.000000e+00 0
## 14 Thyr_Inh_Down Thyr_Inh_Down 1.000000 1.000000e+00 188
## 15 Ret_Inh_Up Thyr_Inh_Down 0.000000 1.000000e+00 0
## 16 Ret_Inh_Down Thyr_Inh_Down 13.053133 8.534049e-02 1
## 17 Andr_Inh_Up Thyr_Inh_Down 0.000000 1.000000e+00 0
## 18 Andr_Inh_Down Thyr_Inh_Down 0.000000 1.000000e+00 0
## 19 GC_Inh_Up Thyr_Inh_Down 0.000000 1.000000e+00 0
## 20 GC_Inh_Down Thyr_Inh_Down 31.989423 3.521227e-63 65
## 21 LivX_Inh_Up Thyr_Inh_Down 0.000000 1.000000e+00 0
## 22 LivX_Inh_Down Thyr_Inh_Down 8.362407 1.912469e-03 4
## 23 AhHyd_Inh_Up Thyr_Inh_Down 0.000000 1.000000e+00 0
## 24 AhHyd_Inh_Down Thyr_Inh_Down 30.931807 1.943615e-09 8
## 25 Thyr_Inh_Up Ret_Inh_Up 0.000000 1.000000e+00 0
## 26 Thyr_Inh_Down Ret_Inh_Up 0.000000 1.000000e+00 0
## 27 Ret_Inh_Up Ret_Inh_Up 1.000000 1.000000e+00 1
## 28 Ret_Inh_Down Ret_Inh_Up 0.000000 1.000000e+00 0
## 29 Andr_Inh_Up Ret_Inh_Up 0.000000 1.000000e+00 0
## 30 Andr_Inh_Down Ret_Inh_Up 0.000000 1.000000e+00 0
## 31 GC_Inh_Up Ret_Inh_Up 0.000000 1.000000e+00 0
## 32 GC_Inh_Down Ret_Inh_Up 0.000000 1.000000e+00 0
## 33 LivX_Inh_Up Ret_Inh_Up 0.000000 1.000000e+00 0
## 34 LivX_Inh_Down Ret_Inh_Up 0.000000 1.000000e+00 0
## 35 AhHyd_Inh_Up Ret_Inh_Up Inf 8.754209e-04 1
## 36 AhHyd_Inh_Down Ret_Inh_Up 0.000000 1.000000e+00 0
## 37 Thyr_Inh_Up Ret_Inh_Down 21.730217 6.511812e-03 2
## 38 Thyr_Inh_Down Ret_Inh_Down 13.053133 8.534049e-02 1
## 39 Ret_Inh_Up Ret_Inh_Down 0.000000 1.000000e+00 0
## 40 Ret_Inh_Down Ret_Inh_Down 1.000000 1.000000e+00 7
## 41 Andr_Inh_Up Ret_Inh_Down 0.000000 1.000000e+00 0
## 42 Andr_Inh_Down Ret_Inh_Down 347.875457 3.765714e-03 1
## 43 GC_Inh_Up Ret_Inh_Down 52.274907 2.241252e-02 1
## 44 GC_Inh_Down Ret_Inh_Down 8.021994 1.344023e-01 1
## 45 LivX_Inh_Up Ret_Inh_Down 0.000000 1.000000e+00 0
## 46 LivX_Inh_Down Ret_Inh_Down 2421.329155 2.462733e-15 6
## 47 AhHyd_Inh_Up Ret_Inh_Down 0.000000 1.000000e+00 0
## 48 AhHyd_Inh_Down Ret_Inh_Down 0.000000 1.000000e+00 0
## 49 Thyr_Inh_Up Andr_Inh_Up 0.000000 1.000000e+00 0
## 50 Thyr_Inh_Down Andr_Inh_Up 0.000000 1.000000e+00 0
## 51 Ret_Inh_Up Andr_Inh_Up 0.000000 1.000000e+00 0
## 52 Ret_Inh_Down Andr_Inh_Up 0.000000 1.000000e+00 0
## 53 Andr_Inh_Up Andr_Inh_Up 1.000000 1.000000e+00 1
## 54 Andr_Inh_Down Andr_Inh_Up 0.000000 1.000000e+00 0
## 55 GC_Inh_Up Andr_Inh_Up 0.000000 1.000000e+00 0
## 56 GC_Inh_Down Andr_Inh_Up 0.000000 1.000000e+00 0
## 57 LivX_Inh_Up Andr_Inh_Up 0.000000 1.000000e+00 0
## 58 LivX_Inh_Down Andr_Inh_Up 0.000000 1.000000e+00 0
## 59 AhHyd_Inh_Up Andr_Inh_Up 0.000000 1.000000e+00 0
## 60 AhHyd_Inh_Down Andr_Inh_Up Inf 1.952862e-03 1
## 61 Thyr_Inh_Up Andr_Inh_Down 32.708898 3.111080e-04 3
## 62 Thyr_Inh_Down Andr_Inh_Down 0.000000 1.000000e+00 0
## 63 Ret_Inh_Up Andr_Inh_Down 0.000000 1.000000e+00 0
## 64 Ret_Inh_Down Andr_Inh_Down 347.875457 3.765714e-03 1
## 65 Andr_Inh_Up Andr_Inh_Down 0.000000 1.000000e+00 0
## 66 Andr_Inh_Down Andr_Inh_Down 1.000000 1.000000e+00 8
## 67 GC_Inh_Up Andr_Inh_Down 333.440509 6.661218e-09 4
## 68 GC_Inh_Down Andr_Inh_Down 6.875475 1.520723e-01 1
## 69 LivX_Inh_Up Andr_Inh_Down 0.000000 1.000000e+00 0
## 70 LivX_Inh_Down Andr_Inh_Down 224.966301 1.166562e-06 3
## 71 AhHyd_Inh_Up Andr_Inh_Down 0.000000 1.000000e+00 0
## 72 AhHyd_Inh_Down Andr_Inh_Down 0.000000 1.000000e+00 0
## 73 Thyr_Inh_Up GC_Inh_Up 37.929142 3.270578e-21 19
## 74 Thyr_Inh_Down GC_Inh_Up 0.000000 1.000000e+00 0
## 75 Ret_Inh_Up GC_Inh_Up 0.000000 1.000000e+00 0
## 76 Ret_Inh_Down GC_Inh_Up 52.274907 2.241252e-02 1
## 77 Andr_Inh_Up GC_Inh_Up 0.000000 1.000000e+00 0
## 78 Andr_Inh_Down GC_Inh_Up 333.440509 6.661218e-09 4
## 79 GC_Inh_Up GC_Inh_Up 1.000000 1.000000e+00 48
## 80 GC_Inh_Down GC_Inh_Up 0.000000 1.000000e+00 0
## 81 LivX_Inh_Up GC_Inh_Up 0.000000 1.000000e+00 0
## 82 LivX_Inh_Down GC_Inh_Up 16.030728 8.112407e-03 2
## 83 AhHyd_Inh_Up GC_Inh_Up 26.197703 4.123119e-02 1
## 84 AhHyd_Inh_Down GC_Inh_Up 0.000000 1.000000e+00 0
## 85 Thyr_Inh_Up GC_Inh_Down 0.000000 1.000000e+00 0
## 86 Thyr_Inh_Down GC_Inh_Down 31.989423 3.521227e-63 65
## 87 Ret_Inh_Up GC_Inh_Down 0.000000 1.000000e+00 0
## 88 Ret_Inh_Down GC_Inh_Down 8.021994 1.344023e-01 1
## 89 Andr_Inh_Up GC_Inh_Down 0.000000 1.000000e+00 0
## 90 Andr_Inh_Down GC_Inh_Down 6.875475 1.520723e-01 1
## 91 GC_Inh_Up GC_Inh_Down 0.000000 1.000000e+00 0
## 92 GC_Inh_Down GC_Inh_Down 1.000000 1.000000e+00 303
## 93 LivX_Inh_Up GC_Inh_Down 0.000000 1.000000e+00 0
## 94 LivX_Inh_Down GC_Inh_Down 15.473027 8.906368e-09 10
## 95 AhHyd_Inh_Up GC_Inh_Down 4.010017 2.351729e-01 1
## 96 AhHyd_Inh_Down GC_Inh_Down 5.583418 2.077014e-02 3
## 97 Thyr_Inh_Up LivX_Inh_Up 0.000000 1.000000e+00 0
## 98 Thyr_Inh_Down LivX_Inh_Up 0.000000 1.000000e+00 0
## 99 Ret_Inh_Up LivX_Inh_Up 0.000000 1.000000e+00 0
## 100 Ret_Inh_Down LivX_Inh_Up 0.000000 1.000000e+00 0
## 101 Andr_Inh_Up LivX_Inh_Up 0.000000 1.000000e+00 0
## 102 Andr_Inh_Down LivX_Inh_Up 0.000000 1.000000e+00 0
## 103 GC_Inh_Up LivX_Inh_Up 0.000000 1.000000e+00 0
## 104 GC_Inh_Down LivX_Inh_Up 0.000000 1.000000e+00 0
## 105 LivX_Inh_Up LivX_Inh_Up 1.000000 1.000000e+00 4
## 106 LivX_Inh_Down LivX_Inh_Up 0.000000 1.000000e+00 0
## 107 AhHyd_Inh_Up LivX_Inh_Up 0.000000 1.000000e+00 0
## 108 AhHyd_Inh_Down LivX_Inh_Up 0.000000 1.000000e+00 0
## 109 Thyr_Inh_Up LivX_Inh_Down 2.712281 1.772825e-01 2
## 110 Thyr_Inh_Down LivX_Inh_Down 8.362407 1.912469e-03 4
## 111 Ret_Inh_Up LivX_Inh_Down 0.000000 1.000000e+00 0
## 112 Ret_Inh_Down LivX_Inh_Down 2421.329155 2.462733e-15 6
## 113 Andr_Inh_Up LivX_Inh_Down 0.000000 1.000000e+00 0
## 114 Andr_Inh_Down LivX_Inh_Down 224.966301 1.166562e-06 3
## 115 GC_Inh_Up LivX_Inh_Down 16.030728 8.112407e-03 2
## 116 GC_Inh_Down LivX_Inh_Down 15.473027 8.906368e-09 10
## 117 LivX_Inh_Up LivX_Inh_Down 0.000000 1.000000e+00 0
## 118 LivX_Inh_Down LivX_Inh_Down 1.000000 1.000000e+00 42
## 119 AhHyd_Inh_Up LivX_Inh_Down 0.000000 1.000000e+00 0
## 120 AhHyd_Inh_Down LivX_Inh_Down 27.338048 3.020683e-03 2
## 121 Thyr_Inh_Up AhHyd_Inh_Up 34.320883 2.187153e-06 5
## 122 Thyr_Inh_Down AhHyd_Inh_Up 0.000000 1.000000e+00 0
## 123 Ret_Inh_Up AhHyd_Inh_Up Inf 8.754209e-04 1
## 124 Ret_Inh_Down AhHyd_Inh_Up 0.000000 1.000000e+00 0
## 125 Andr_Inh_Up AhHyd_Inh_Up 0.000000 1.000000e+00 0
## 126 Andr_Inh_Down AhHyd_Inh_Up 0.000000 1.000000e+00 0
## 127 GC_Inh_Up AhHyd_Inh_Up 26.197703 4.123119e-02 1
## 128 GC_Inh_Down AhHyd_Inh_Up 4.010017 2.351729e-01 1
## 129 LivX_Inh_Up AhHyd_Inh_Up 0.000000 1.000000e+00 0
## 130 LivX_Inh_Down AhHyd_Inh_Up 0.000000 1.000000e+00 0
## 131 AhHyd_Inh_Up AhHyd_Inh_Up 1.000000 1.000000e+00 13
## 132 AhHyd_Inh_Down AhHyd_Inh_Up 0.000000 1.000000e+00 0
## 133 Thyr_Inh_Up AhHyd_Inh_Down 0.000000 1.000000e+00 0
## 134 Thyr_Inh_Down AhHyd_Inh_Down 30.931807 1.943615e-09 8
## 135 Ret_Inh_Up AhHyd_Inh_Down 0.000000 1.000000e+00 0
## 136 Ret_Inh_Down AhHyd_Inh_Down 0.000000 1.000000e+00 0
## 137 Andr_Inh_Up AhHyd_Inh_Down Inf 1.952862e-03 1
## 138 Andr_Inh_Down AhHyd_Inh_Down 0.000000 1.000000e+00 0
## 139 GC_Inh_Up AhHyd_Inh_Down 0.000000 1.000000e+00 0
## 140 GC_Inh_Down AhHyd_Inh_Down 5.583418 2.077014e-02 3
## 141 LivX_Inh_Up AhHyd_Inh_Down 0.000000 1.000000e+00 0
## 142 LivX_Inh_Down AhHyd_Inh_Down 27.338048 3.020683e-03 2
## 143 AhHyd_Inh_Up AhHyd_Inh_Down 0.000000 1.000000e+00 0
## 144 AhHyd_Inh_Down AhHyd_Inh_Down 1.000000 1.000000e+00 29DotPlot: visualization
I select as significant overlaps having an OR > 2 and at least 25 overlapping genes. Dots are shown for PVals < 0.01 (set in the plot). Max value in the plot must be set according to minimum PVal to avoid dots not to be shown.
ResSel <- dplyr::filter(ResMod, OR > 2) %>% dplyr::filter(Numbers > 25)
min(ResSel$Pval)## [1] 3.521227e-63max(ResSel$OR)## [1] 31.98942Dot <- ggplot(ResSel, aes(DEGs, KBase, label=Numbers)) +
geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1)) +
ggtitle('Overlap across Inhibitor-modulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_Inhibitor.pdf'), width=8, height=8)4.3 Visualize overlap results selectively for retinoic, liverX, thyroid
Selection
Path <- c('Thyr_Inh_Up', 'Thyr_Inh_Down', 'Ret_Inh_Up', 'Ret_Inh_Down', 'LivX_Inh_Up', 'LivX_Inh_Down')
ResPath <- ResSel[ResSel$DEGs %in% Path & ResSel$KBase %in% Path, ]
ResPath
## [1] DEGs KBase OR Pval Numbers
## <0 rows> (or 0-length row.names)No significant overlap found.
5. Comparison across pathways: up-regulated genes
5.1 Perform the overlap
DEGs_UpReg <- list(
Thyr_Ag= row.names(DEA$Thyr$Agonist$DEGs[DEA$Thyr$Agonist$DEGs$log2FoldChange > 0, ]),
Thyr_Inh= row.names(DEA$Thyr$Inhibitor$DEGs[DEA$Thyr$Inhibitor$DEGs$log2FoldChange > 0, ]),
Ret_Ag= row.names(DEA$Ret$Agonist$DEGs[DEA$Ret$Agonist$DEGs$log2FoldChange > 0, ]),
Ret_Inh= row.names(DEA$Ret$Inhibitor$DEGs[DEA$Ret$Inhibitor$DEGs$log2FoldChange > 0, ]),
Estr_Ag= row.names(DEA$Estr$Agonist$DEGs[DEA$Estr$Agonist$DEGs$log2FoldChange > 0, ]),
Andr_Ag= row.names(DEA$Andr$Agonist$DEGs[DEA$Andr$Agonist$DEGs$log2FoldChange > 0, ]),
Andr_Inh= row.names(DEA$Andr$Inhibitor$DEGs[DEA$Andr$Inhibitor$DEGs$log2FoldChange > 0, ]),
GC_Ag= row.names(DEA$GC$Agonist$DEGs[DEA$GC$Agonist$DEGs$log2FoldChange > 0, ]),
GC_Inh= row.names(DEA$GC$Inhibitor$DEGs[DEA$GC$Inhibitor$DEGs$log2FoldChange > 0, ]),
LivX_Ag= row.names(DEA$LivX$Agonist$DEGs[DEA$LivX$Agonist$DEGs$log2FoldChange > 0, ]),
LivX_Inh= row.names(DEA$LivX$Inhibitor$DEGs[DEA$LivX$Inhibitor$DEGs$log2FoldChange > 0, ]),
AhHyd_Ag= row.names(DEA$AhHyd$Agonist$DEGs[DEA$AhHyd$Agonist$DEGs$log2FoldChange > 0, ]),
AhHyd_Inh= row.names(DEA$AhHyd$Inhibitor$DEGs[DEA$AhHyd$Inhibitor$DEGs$log2FoldChange > 0, ])
)Universe <- row.names(DEA$Ret$Inhibitor$Res) %>% unique()
length(Universe)
## [1] 14850OvObj <- newGOM(DEGs_UpReg, DEGs_UpReg, genome.size=length(Universe))
print(OvObj)
## A GeneOverlapMatrix object:
## ###### Intersection ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Andr_Ag Andr_Inh GC_Ag GC_Inh
## Thyr_Ag 142 14 81 0 84 5 0 0 0
## Thyr_Inh 14 270 80 0 39 2 0 0 19
## Ret_Ag 81 80 1677 0 462 4 0 1 13
## Ret_Inh 0 0 0 1 0 0 0 0 0
## Estr_Ag 84 39 462 0 905 4 0 1 2
## Andr_Ag 5 2 4 0 4 6 0 0 0
## Andr_Inh 0 0 0 0 0 0 1 0 0
## GC_Ag 0 0 1 0 1 0 0 6 0
## GC_Inh 0 19 13 0 2 0 0 0 48
## LivX_Ag 56 64 367 0 219 5 0 0 5
## LivX_Inh 0 0 0 0 0 0 0 0 0
## AhHyd_Ag 0 0 0 0 0 0 0 0 0
## AhHyd_Inh 4 5 10 1 8 2 0 0 1
## LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 56 0 0 4
## Thyr_Inh 64 0 0 5
## Ret_Ag 367 0 0 10
## Ret_Inh 0 0 0 1
## Estr_Ag 219 0 0 8
## Andr_Ag 5 0 0 2
## Andr_Inh 0 0 0 0
## GC_Ag 0 0 0 0
## GC_Inh 5 0 0 1
## LivX_Ag 450 0 0 10
## LivX_Inh 0 4 0 0
## AhHyd_Ag 0 0 3 0
## AhHyd_Inh 10 0 0 13
## ###### P-value ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag
## Thyr_Ag 0.000000e+00 3.098622e-07 3.063677e-40 1.000000e+00 2.641447e-65
## Thyr_Inh 3.098622e-07 0.000000e+00 1.283202e-16 1.000000e+00 4.298987e-07
## Ret_Ag 3.063677e-40 1.283202e-16 0.000000e+00 1.000000e+00 3.762356e-212
## Ret_Inh 1.000000e+00 1.000000e+00 1.000000e+00 6.734007e-05 1.000000e+00
## Estr_Ag 2.641447e-65 4.298987e-07 3.762356e-212 1.000000e+00 0.000000e+00
## Andr_Ag 4.435963e-10 4.707606e-03 2.013961e-03 1.000000e+00 1.861609e-04
## Andr_Inh 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## GC_Ag 1.000000e+00 1.000000e+00 5.128154e-01 1.000000e+00 3.143162e-01
## GC_Inh 1.000000e+00 3.270578e-21 2.001744e-03 1.000000e+00 7.992924e-01
## LivX_Ag 4.556114e-48 2.868436e-39 1.730574e-276 1.000000e+00 1.688829e-149
## LivX_Inh 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## AhHyd_Ag 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## AhHyd_Inh 5.358972e-06 2.187153e-06 6.821193e-08 8.754209e-04 1.805333e-07
## Andr_Ag Andr_Inh GC_Ag GC_Inh LivX_Ag
## Thyr_Ag 4.435963e-10 1.000000e+00 1.000000e+00 1.000000e+00 4.556114e-48
## Thyr_Inh 4.707606e-03 1.000000e+00 1.000000e+00 3.270578e-21 2.868436e-39
## Ret_Ag 2.013961e-03 1.000000e+00 5.128154e-01 2.001744e-03 1.730574e-276
## Ret_Inh 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## Estr_Ag 1.861609e-04 1.000000e+00 3.143162e-01 7.992924e-01 1.688829e-149
## Andr_Ag 6.720669e-23 1.000000e+00 1.000000e+00 1.000000e+00 1.462864e-07
## Andr_Inh 1.000000e+00 6.734007e-05 1.000000e+00 1.000000e+00 1.000000e+00
## GC_Ag 1.000000e+00 1.000000e+00 6.720669e-23 1.000000e+00 1.000000e+00
## GC_Inh 1.000000e+00 1.000000e+00 1.000000e+00 7.657078e-140 1.467358e-02
## LivX_Ag 1.462864e-07 1.000000e+00 1.000000e+00 1.467358e-02 0.000000e+00
## LivX_Inh 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## AhHyd_Ag 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## AhHyd_Inh 1.059093e-05 1.000000e+00 1.000000e+00 4.123119e-02 1.560309e-13
## LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 1.000000e+00 1.000000e+00 5.358972e-06
## Thyr_Inh 1.000000e+00 1.000000e+00 2.187153e-06
## Ret_Ag 1.000000e+00 1.000000e+00 6.821193e-08
## Ret_Inh 1.000000e+00 1.000000e+00 8.754209e-04
## Estr_Ag 1.000000e+00 1.000000e+00 1.805333e-07
## Andr_Ag 1.000000e+00 1.000000e+00 1.059093e-05
## Andr_Inh 1.000000e+00 1.000000e+00 1.000000e+00
## GC_Ag 1.000000e+00 1.000000e+00 1.000000e+00
## GC_Inh 1.000000e+00 1.000000e+00 4.123119e-02
## LivX_Ag 1.000000e+00 1.000000e+00 1.560309e-13
## LivX_Inh 4.937202e-16 1.000000e+00 1.000000e+00
## AhHyd_Ag 1.000000e+00 1.832566e-12 1.000000e+00
## AhHyd_Inh 1.000000e+00 1.000000e+00 3.665373e-45
## ###### Odds Ratio ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Andr_Ag Andr_Inh
## Thyr_Ag Inf 6.172620 10.905715 0 24.4691632 533.98796 0
## Thyr_Inh 6.17262 Inf 3.422680 0 2.6732328 27.14732 0
## Ret_Ag 10.90572 3.422680 Inf 0 10.9234073 15.73955 0
## Ret_Inh 0.00000 0.000000 0.000000 Inf 0.0000000 0.00000 0
## Estr_Ag 24.46916 2.673233 10.923407 0 Inf 30.94356 0
## Andr_Ag 533.98796 27.147324 15.739550 0 30.9435619 Inf 0
## Andr_Inh 0.00000 0.000000 0.000000 0 0.0000000 0.00000 Inf
## GC_Ag 0.00000 0.000000 1.571291 0 3.0836743 0.00000 0
## GC_Inh 0.00000 37.929142 2.932290 0 0.6692207 0.00000 0
## LivX_Ag 23.63592 11.422165 44.201409 0 18.9463251 161.91079 0
## LivX_Inh 0.00000 0.000000 0.000000 0 0.0000000 0.00000 0
## AhHyd_Ag 0.00000 0.000000 0.000000 0 0.0000000 0.00000 0
## AhHyd_Inh 47.22207 34.320883 26.322839 Inf 24.8479088 652.32891 0
## GC_Ag GC_Inh LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 0.000000 0.0000000 23.635922 0 0 47.22207
## Thyr_Inh 0.000000 37.9291424 11.422165 0 0 34.32088
## Ret_Ag 1.571291 2.9322904 44.201409 0 0 26.32284
## Ret_Inh 0.000000 0.0000000 0.000000 0 0 Inf
## Estr_Ag 3.083674 0.6692207 18.946325 0 0 24.84791
## Andr_Ag 0.000000 0.0000000 161.910790 0 0 652.32891
## Andr_Inh 0.000000 0.0000000 0.000000 0 0 0.00000
## GC_Ag Inf 0.0000000 0.000000 0 0 0.00000
## GC_Inh 0.000000 Inf 3.751219 0 0 26.19770
## LivX_Ag 0.000000 3.7512195 Inf 0 0 108.70227
## LivX_Inh 0.000000 0.0000000 0.000000 Inf 0 0.00000
## AhHyd_Ag 0.000000 0.0000000 0.000000 0 Inf 0.00000
## AhHyd_Inh 0.000000 26.1977029 108.702275 0 0 Inf
## ###### Jaccard Index ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Andr_Ag
## Thyr_Ag 1.00000000 0.03517588 0.0466052934 0.00000000 0.087227414 0.034965035
## Thyr_Inh 0.03517588 1.00000000 0.0428494912 0.00000000 0.034330986 0.007299270
## Ret_Ag 0.04660529 0.04284949 1.0000000000 0.00000000 0.217924528 0.002382370
## Ret_Inh 0.00000000 0.00000000 0.0000000000 1.00000000 0.000000000 0.000000000
## Estr_Ag 0.08722741 0.03433099 0.2179245283 0.00000000 1.000000000 0.004410143
## Andr_Ag 0.03496503 0.00729927 0.0023823705 0.00000000 0.004410143 1.000000000
## Andr_Inh 0.00000000 0.00000000 0.0000000000 0.00000000 0.000000000 0.000000000
## GC_Ag 0.00000000 0.00000000 0.0005945303 0.00000000 0.001098901 0.000000000
## GC_Inh 0.00000000 0.06354515 0.0075934579 0.00000000 0.002103049 0.000000000
## LivX_Ag 0.10447761 0.09756098 0.2085227273 0.00000000 0.192781690 0.011086475
## LivX_Inh 0.00000000 0.00000000 0.0000000000 0.00000000 0.000000000 0.000000000
## AhHyd_Ag 0.00000000 0.00000000 0.0000000000 0.00000000 0.000000000 0.000000000
## AhHyd_Inh 0.02649007 0.01798561 0.0059523810 0.07692308 0.008791209 0.117647059
## Andr_Inh GC_Ag GC_Inh LivX_Ag LivX_Inh AhHyd_Ag
## Thyr_Ag 0 0.0000000000 0.000000000 0.10447761 0 0
## Thyr_Inh 0 0.0000000000 0.063545151 0.09756098 0 0
## Ret_Ag 0 0.0005945303 0.007593458 0.20852273 0 0
## Ret_Inh 0 0.0000000000 0.000000000 0.00000000 0 0
## Estr_Ag 0 0.0010989011 0.002103049 0.19278169 0 0
## Andr_Ag 0 0.0000000000 0.000000000 0.01108647 0 0
## Andr_Inh 1 0.0000000000 0.000000000 0.00000000 0 0
## GC_Ag 0 1.0000000000 0.000000000 0.00000000 0 0
## GC_Inh 0 0.0000000000 1.000000000 0.01014199 0 0
## LivX_Ag 0 0.0000000000 0.010141988 1.00000000 0 0
## LivX_Inh 0 0.0000000000 0.000000000 0.00000000 1 0
## AhHyd_Ag 0 0.0000000000 0.000000000 0.00000000 0 1
## AhHyd_Inh 0 0.0000000000 0.016666667 0.02207506 0 0
## AhHyd_Inh
## Thyr_Ag 0.026490066
## Thyr_Inh 0.017985612
## Ret_Ag 0.005952381
## Ret_Inh 0.076923077
## Estr_Ag 0.008791209
## Andr_Ag 0.117647059
## Andr_Inh 0.000000000
## GC_Ag 0.000000000
## GC_Inh 0.016666667
## LivX_Ag 0.022075055
## LivX_Inh 0.000000000
## AhHyd_Ag 0.000000000
## AhHyd_Inh 1.000000000getMatrix(OvObj, name='intersection')
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Andr_Ag Andr_Inh GC_Ag GC_Inh
## Thyr_Ag 142 14 81 0 84 5 0 0 0
## Thyr_Inh 14 270 80 0 39 2 0 0 19
## Ret_Ag 81 80 1677 0 462 4 0 1 13
## Ret_Inh 0 0 0 1 0 0 0 0 0
## Estr_Ag 84 39 462 0 905 4 0 1 2
## Andr_Ag 5 2 4 0 4 6 0 0 0
## Andr_Inh 0 0 0 0 0 0 1 0 0
## GC_Ag 0 0 1 0 1 0 0 6 0
## GC_Inh 0 19 13 0 2 0 0 0 48
## LivX_Ag 56 64 367 0 219 5 0 0 5
## LivX_Inh 0 0 0 0 0 0 0 0 0
## AhHyd_Ag 0 0 0 0 0 0 0 0 0
## AhHyd_Inh 4 5 10 1 8 2 0 0 1
## LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 56 0 0 4
## Thyr_Inh 64 0 0 5
## Ret_Ag 367 0 0 10
## Ret_Inh 0 0 0 1
## Estr_Ag 219 0 0 8
## Andr_Ag 5 0 0 2
## Andr_Inh 0 0 0 0
## GC_Ag 0 0 0 0
## GC_Inh 5 0 0 1
## LivX_Ag 450 0 0 10
## LivX_Inh 0 4 0 0
## AhHyd_Ag 0 0 3 0
## AhHyd_Inh 10 0 0 13getMatrix(OvObj, name='pval')
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag
## Thyr_Ag 0.000000e+00 3.098622e-07 3.063677e-40 1.000000e+00 2.641447e-65
## Thyr_Inh 3.098622e-07 0.000000e+00 1.283202e-16 1.000000e+00 4.298987e-07
## Ret_Ag 3.063677e-40 1.283202e-16 0.000000e+00 1.000000e+00 3.762356e-212
## Ret_Inh 1.000000e+00 1.000000e+00 1.000000e+00 6.734007e-05 1.000000e+00
## Estr_Ag 2.641447e-65 4.298987e-07 3.762356e-212 1.000000e+00 0.000000e+00
## Andr_Ag 4.435963e-10 4.707606e-03 2.013961e-03 1.000000e+00 1.861609e-04
## Andr_Inh 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## GC_Ag 1.000000e+00 1.000000e+00 5.128154e-01 1.000000e+00 3.143162e-01
## GC_Inh 1.000000e+00 3.270578e-21 2.001744e-03 1.000000e+00 7.992924e-01
## LivX_Ag 4.556114e-48 2.868436e-39 1.730574e-276 1.000000e+00 1.688829e-149
## LivX_Inh 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## AhHyd_Ag 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## AhHyd_Inh 5.358972e-06 2.187153e-06 6.821193e-08 8.754209e-04 1.805333e-07
## Andr_Ag Andr_Inh GC_Ag GC_Inh LivX_Ag
## Thyr_Ag 4.435963e-10 1.000000e+00 1.000000e+00 1.000000e+00 4.556114e-48
## Thyr_Inh 4.707606e-03 1.000000e+00 1.000000e+00 3.270578e-21 2.868436e-39
## Ret_Ag 2.013961e-03 1.000000e+00 5.128154e-01 2.001744e-03 1.730574e-276
## Ret_Inh 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## Estr_Ag 1.861609e-04 1.000000e+00 3.143162e-01 7.992924e-01 1.688829e-149
## Andr_Ag 6.720669e-23 1.000000e+00 1.000000e+00 1.000000e+00 1.462864e-07
## Andr_Inh 1.000000e+00 6.734007e-05 1.000000e+00 1.000000e+00 1.000000e+00
## GC_Ag 1.000000e+00 1.000000e+00 6.720669e-23 1.000000e+00 1.000000e+00
## GC_Inh 1.000000e+00 1.000000e+00 1.000000e+00 7.657078e-140 1.467358e-02
## LivX_Ag 1.462864e-07 1.000000e+00 1.000000e+00 1.467358e-02 0.000000e+00
## LivX_Inh 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## AhHyd_Ag 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
## AhHyd_Inh 1.059093e-05 1.000000e+00 1.000000e+00 4.123119e-02 1.560309e-13
## LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 1.000000e+00 1.000000e+00 5.358972e-06
## Thyr_Inh 1.000000e+00 1.000000e+00 2.187153e-06
## Ret_Ag 1.000000e+00 1.000000e+00 6.821193e-08
## Ret_Inh 1.000000e+00 1.000000e+00 8.754209e-04
## Estr_Ag 1.000000e+00 1.000000e+00 1.805333e-07
## Andr_Ag 1.000000e+00 1.000000e+00 1.059093e-05
## Andr_Inh 1.000000e+00 1.000000e+00 1.000000e+00
## GC_Ag 1.000000e+00 1.000000e+00 1.000000e+00
## GC_Inh 1.000000e+00 1.000000e+00 4.123119e-02
## LivX_Ag 1.000000e+00 1.000000e+00 1.560309e-13
## LivX_Inh 4.937202e-16 1.000000e+00 1.000000e+00
## AhHyd_Ag 1.000000e+00 1.832566e-12 1.000000e+00
## AhHyd_Inh 1.000000e+00 1.000000e+00 3.665373e-45getMatrix(OvObj, name='odds.ratio')
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Andr_Ag Andr_Inh
## Thyr_Ag Inf 6.172620 10.905715 0 24.4691632 533.98796 0
## Thyr_Inh 6.17262 Inf 3.422680 0 2.6732328 27.14732 0
## Ret_Ag 10.90572 3.422680 Inf 0 10.9234073 15.73955 0
## Ret_Inh 0.00000 0.000000 0.000000 Inf 0.0000000 0.00000 0
## Estr_Ag 24.46916 2.673233 10.923407 0 Inf 30.94356 0
## Andr_Ag 533.98796 27.147324 15.739550 0 30.9435619 Inf 0
## Andr_Inh 0.00000 0.000000 0.000000 0 0.0000000 0.00000 Inf
## GC_Ag 0.00000 0.000000 1.571291 0 3.0836743 0.00000 0
## GC_Inh 0.00000 37.929142 2.932290 0 0.6692207 0.00000 0
## LivX_Ag 23.63592 11.422165 44.201409 0 18.9463251 161.91079 0
## LivX_Inh 0.00000 0.000000 0.000000 0 0.0000000 0.00000 0
## AhHyd_Ag 0.00000 0.000000 0.000000 0 0.0000000 0.00000 0
## AhHyd_Inh 47.22207 34.320883 26.322839 Inf 24.8479088 652.32891 0
## GC_Ag GC_Inh LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 0.000000 0.0000000 23.635922 0 0 47.22207
## Thyr_Inh 0.000000 37.9291424 11.422165 0 0 34.32088
## Ret_Ag 1.571291 2.9322904 44.201409 0 0 26.32284
## Ret_Inh 0.000000 0.0000000 0.000000 0 0 Inf
## Estr_Ag 3.083674 0.6692207 18.946325 0 0 24.84791
## Andr_Ag 0.000000 0.0000000 161.910790 0 0 652.32891
## Andr_Inh 0.000000 0.0000000 0.000000 0 0 0.00000
## GC_Ag Inf 0.0000000 0.000000 0 0 0.00000
## GC_Inh 0.000000 Inf 3.751219 0 0 26.19770
## LivX_Ag 0.000000 3.7512195 Inf 0 0 108.70227
## LivX_Inh 0.000000 0.0000000 0.000000 Inf 0 0.00000
## AhHyd_Ag 0.000000 0.0000000 0.000000 0 Inf 0.00000
## AhHyd_Inh 0.000000 26.1977029 108.702275 0 0 Inf5.2 Visualize overlap results
DotPlot: data preparation
OR <- data.frame(getMatrix(OvObj, name='odds.ratio'))
OR$DEGs <- row.names(OR)
OR <- gather(OR, 'KBase', 'OR', -DEGs)
PVAL <- data.frame(getMatrix(OvObj, name='pval'))
PVAL$DEGs <- row.names(PVAL)
PVAL <- gather(PVAL, 'KBase', 'PVal', -DEGs)
NUM <- data.frame(getMatrix(OvObj, name='intersection'))
NUM$DEGs <- row.names(NUM)
NUM <- gather(NUM, 'KBase', 'Numbers', -DEGs)
if(! identical(OR$DEGs, PVAL$DEGs)){
stop('Inconsistecy')
}
if(! identical(OR$DEGs, NUM$DEGs)){
stop('Inconsistecy')
}
if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}
if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}
Res <- mutate(OR, Pval=PVAL$PVal) %>% mutate(Numbers=NUM$Numbers)
Res
## DEGs KBase OR Pval Numbers
## 1 Thyr_Ag Thyr_Ag Inf 0.000000e+00 142
## 2 Thyr_Inh Thyr_Ag 6.1726199 3.098622e-07 14
## 3 Ret_Ag Thyr_Ag 10.9057151 3.063677e-40 81
## 4 Ret_Inh Thyr_Ag 0.0000000 1.000000e+00 0
## 5 Estr_Ag Thyr_Ag 24.4691632 2.641447e-65 84
## 6 Andr_Ag Thyr_Ag 533.9879643 4.435963e-10 5
## 7 Andr_Inh Thyr_Ag 0.0000000 1.000000e+00 0
## 8 GC_Ag Thyr_Ag 0.0000000 1.000000e+00 0
## 9 GC_Inh Thyr_Ag 0.0000000 1.000000e+00 0
## 10 LivX_Ag Thyr_Ag 23.6359221 4.556114e-48 56
## 11 LivX_Inh Thyr_Ag 0.0000000 1.000000e+00 0
## 12 AhHyd_Ag Thyr_Ag 0.0000000 1.000000e+00 0
## 13 AhHyd_Inh Thyr_Ag 47.2220668 5.358972e-06 4
## 14 Thyr_Ag Thyr_Inh 6.1726199 3.098622e-07 14
## 15 Thyr_Inh Thyr_Inh Inf 0.000000e+00 270
## 16 Ret_Ag Thyr_Inh 3.4226795 1.283202e-16 80
## 17 Ret_Inh Thyr_Inh 0.0000000 1.000000e+00 0
## 18 Estr_Ag Thyr_Inh 2.6732328 4.298987e-07 39
## 19 Andr_Ag Thyr_Inh 27.1473236 4.707606e-03 2
## 20 Andr_Inh Thyr_Inh 0.0000000 1.000000e+00 0
## 21 GC_Ag Thyr_Inh 0.0000000 1.000000e+00 0
## 22 GC_Inh Thyr_Inh 37.9291424 3.270578e-21 19
## 23 LivX_Ag Thyr_Inh 11.4221654 2.868436e-39 64
## 24 LivX_Inh Thyr_Inh 0.0000000 1.000000e+00 0
## 25 AhHyd_Ag Thyr_Inh 0.0000000 1.000000e+00 0
## 26 AhHyd_Inh Thyr_Inh 34.3208830 2.187153e-06 5
## 27 Thyr_Ag Ret_Ag 10.9057151 3.063677e-40 81
## 28 Thyr_Inh Ret_Ag 3.4226795 1.283202e-16 80
## 29 Ret_Ag Ret_Ag Inf 0.000000e+00 1677
## 30 Ret_Inh Ret_Ag 0.0000000 1.000000e+00 0
## 31 Estr_Ag Ret_Ag 10.9234073 3.762356e-212 462
## 32 Andr_Ag Ret_Ag 15.7395497 2.013961e-03 4
## 33 Andr_Inh Ret_Ag 0.0000000 1.000000e+00 0
## 34 GC_Ag Ret_Ag 1.5712909 5.128154e-01 1
## 35 GC_Inh Ret_Ag 2.9322904 2.001744e-03 13
## 36 LivX_Ag Ret_Ag 44.2014086 1.730574e-276 367
## 37 LivX_Inh Ret_Ag 0.0000000 1.000000e+00 0
## 38 AhHyd_Ag Ret_Ag 0.0000000 1.000000e+00 0
## 39 AhHyd_Inh Ret_Ag 26.3228390 6.821193e-08 10
## 40 Thyr_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 41 Thyr_Inh Ret_Inh 0.0000000 1.000000e+00 0
## 42 Ret_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 43 Ret_Inh Ret_Inh Inf 6.734007e-05 1
## 44 Estr_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 45 Andr_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 46 Andr_Inh Ret_Inh 0.0000000 1.000000e+00 0
## 47 GC_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 48 GC_Inh Ret_Inh 0.0000000 1.000000e+00 0
## 49 LivX_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 50 LivX_Inh Ret_Inh 0.0000000 1.000000e+00 0
## 51 AhHyd_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 52 AhHyd_Inh Ret_Inh Inf 8.754209e-04 1
## 53 Thyr_Ag Estr_Ag 24.4691632 2.641447e-65 84
## 54 Thyr_Inh Estr_Ag 2.6732328 4.298987e-07 39
## 55 Ret_Ag Estr_Ag 10.9234073 3.762356e-212 462
## 56 Ret_Inh Estr_Ag 0.0000000 1.000000e+00 0
## 57 Estr_Ag Estr_Ag Inf 0.000000e+00 905
## 58 Andr_Ag Estr_Ag 30.9435619 1.861609e-04 4
## 59 Andr_Inh Estr_Ag 0.0000000 1.000000e+00 0
## 60 GC_Ag Estr_Ag 3.0836743 3.143162e-01 1
## 61 GC_Inh Estr_Ag 0.6692207 7.992924e-01 2
## 62 LivX_Ag Estr_Ag 18.9463251 1.688829e-149 219
## 63 LivX_Inh Estr_Ag 0.0000000 1.000000e+00 0
## 64 AhHyd_Ag Estr_Ag 0.0000000 1.000000e+00 0
## 65 AhHyd_Inh Estr_Ag 24.8479088 1.805333e-07 8
## 66 Thyr_Ag Andr_Ag 533.9879643 4.435963e-10 5
## 67 Thyr_Inh Andr_Ag 27.1473236 4.707606e-03 2
## 68 Ret_Ag Andr_Ag 15.7395497 2.013961e-03 4
## 69 Ret_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 70 Estr_Ag Andr_Ag 30.9435619 1.861609e-04 4
## 71 Andr_Ag Andr_Ag Inf 6.720669e-23 6
## 72 Andr_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 73 GC_Ag Andr_Ag 0.0000000 1.000000e+00 0
## 74 GC_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 75 LivX_Ag Andr_Ag 161.9107898 1.462864e-07 5
## 76 LivX_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 77 AhHyd_Ag Andr_Ag 0.0000000 1.000000e+00 0
## 78 AhHyd_Inh Andr_Ag 652.3289113 1.059093e-05 2
## 79 Thyr_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 80 Thyr_Inh Andr_Inh 0.0000000 1.000000e+00 0
## 81 Ret_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 82 Ret_Inh Andr_Inh 0.0000000 1.000000e+00 0
## 83 Estr_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 84 Andr_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 85 Andr_Inh Andr_Inh Inf 6.734007e-05 1
## 86 GC_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 87 GC_Inh Andr_Inh 0.0000000 1.000000e+00 0
## 88 LivX_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 89 LivX_Inh Andr_Inh 0.0000000 1.000000e+00 0
## 90 AhHyd_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 91 AhHyd_Inh Andr_Inh 0.0000000 1.000000e+00 0
## 92 Thyr_Ag GC_Ag 0.0000000 1.000000e+00 0
## 93 Thyr_Inh GC_Ag 0.0000000 1.000000e+00 0
## 94 Ret_Ag GC_Ag 1.5712909 5.128154e-01 1
## 95 Ret_Inh GC_Ag 0.0000000 1.000000e+00 0
## 96 Estr_Ag GC_Ag 3.0836743 3.143162e-01 1
## 97 Andr_Ag GC_Ag 0.0000000 1.000000e+00 0
## 98 Andr_Inh GC_Ag 0.0000000 1.000000e+00 0
## 99 GC_Ag GC_Ag Inf 6.720669e-23 6
## 100 GC_Inh GC_Ag 0.0000000 1.000000e+00 0
## 101 LivX_Ag GC_Ag 0.0000000 1.000000e+00 0
## 102 LivX_Inh GC_Ag 0.0000000 1.000000e+00 0
## 103 AhHyd_Ag GC_Ag 0.0000000 1.000000e+00 0
## 104 AhHyd_Inh GC_Ag 0.0000000 1.000000e+00 0
## 105 Thyr_Ag GC_Inh 0.0000000 1.000000e+00 0
## 106 Thyr_Inh GC_Inh 37.9291424 3.270578e-21 19
## 107 Ret_Ag GC_Inh 2.9322904 2.001744e-03 13
## 108 Ret_Inh GC_Inh 0.0000000 1.000000e+00 0
## 109 Estr_Ag GC_Inh 0.6692207 7.992924e-01 2
## 110 Andr_Ag GC_Inh 0.0000000 1.000000e+00 0
## 111 Andr_Inh GC_Inh 0.0000000 1.000000e+00 0
## 112 GC_Ag GC_Inh 0.0000000 1.000000e+00 0
## 113 GC_Inh GC_Inh Inf 7.657078e-140 48
## 114 LivX_Ag GC_Inh 3.7512195 1.467358e-02 5
## 115 LivX_Inh GC_Inh 0.0000000 1.000000e+00 0
## 116 AhHyd_Ag GC_Inh 0.0000000 1.000000e+00 0
## 117 AhHyd_Inh GC_Inh 26.1977029 4.123119e-02 1
## 118 Thyr_Ag LivX_Ag 23.6359221 4.556114e-48 56
## 119 Thyr_Inh LivX_Ag 11.4221654 2.868436e-39 64
## 120 Ret_Ag LivX_Ag 44.2014086 1.730574e-276 367
## 121 Ret_Inh LivX_Ag 0.0000000 1.000000e+00 0
## 122 Estr_Ag LivX_Ag 18.9463251 1.688829e-149 219
## 123 Andr_Ag LivX_Ag 161.9107898 1.462864e-07 5
## 124 Andr_Inh LivX_Ag 0.0000000 1.000000e+00 0
## 125 GC_Ag LivX_Ag 0.0000000 1.000000e+00 0
## 126 GC_Inh LivX_Ag 3.7512195 1.467358e-02 5
## 127 LivX_Ag LivX_Ag Inf 0.000000e+00 450
## 128 LivX_Inh LivX_Ag 0.0000000 1.000000e+00 0
## 129 AhHyd_Ag LivX_Ag 0.0000000 1.000000e+00 0
## 130 AhHyd_Inh LivX_Ag 108.7022748 1.560309e-13 10
## 131 Thyr_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 132 Thyr_Inh LivX_Inh 0.0000000 1.000000e+00 0
## 133 Ret_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 134 Ret_Inh LivX_Inh 0.0000000 1.000000e+00 0
## 135 Estr_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 136 Andr_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 137 Andr_Inh LivX_Inh 0.0000000 1.000000e+00 0
## 138 GC_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 139 GC_Inh LivX_Inh 0.0000000 1.000000e+00 0
## 140 LivX_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 141 LivX_Inh LivX_Inh Inf 4.937202e-16 4
## 142 AhHyd_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 143 AhHyd_Inh LivX_Inh 0.0000000 1.000000e+00 0
## 144 Thyr_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 145 Thyr_Inh AhHyd_Ag 0.0000000 1.000000e+00 0
## 146 Ret_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 147 Ret_Inh AhHyd_Ag 0.0000000 1.000000e+00 0
## 148 Estr_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 149 Andr_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 150 Andr_Inh AhHyd_Ag 0.0000000 1.000000e+00 0
## 151 GC_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 152 GC_Inh AhHyd_Ag 0.0000000 1.000000e+00 0
## 153 LivX_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 154 LivX_Inh AhHyd_Ag 0.0000000 1.000000e+00 0
## 155 AhHyd_Ag AhHyd_Ag Inf 1.832566e-12 3
## 156 AhHyd_Inh AhHyd_Ag 0.0000000 1.000000e+00 0
## 157 Thyr_Ag AhHyd_Inh 47.2220668 5.358972e-06 4
## 158 Thyr_Inh AhHyd_Inh 34.3208830 2.187153e-06 5
## 159 Ret_Ag AhHyd_Inh 26.3228390 6.821193e-08 10
## 160 Ret_Inh AhHyd_Inh Inf 8.754209e-04 1
## 161 Estr_Ag AhHyd_Inh 24.8479088 1.805333e-07 8
## 162 Andr_Ag AhHyd_Inh 652.3289113 1.059093e-05 2
## 163 Andr_Inh AhHyd_Inh 0.0000000 1.000000e+00 0
## 164 GC_Ag AhHyd_Inh 0.0000000 1.000000e+00 0
## 165 GC_Inh AhHyd_Inh 26.1977029 4.123119e-02 1
## 166 LivX_Ag AhHyd_Inh 108.7022748 1.560309e-13 10
## 167 LivX_Inh AhHyd_Inh 0.0000000 1.000000e+00 0
## 168 AhHyd_Ag AhHyd_Inh 0.0000000 1.000000e+00 0
## 169 AhHyd_Inh AhHyd_Inh Inf 3.665373e-45 13ResMod <- Res
ResMod[ResMod$DEGs == ResMod$KBase, ]$OR <- 1
ResMod[ResMod$DEGs == ResMod$KBase, ]$Pval <- 1
ResMod
## DEGs KBase OR Pval Numbers
## 1 Thyr_Ag Thyr_Ag 1.0000000 1.000000e+00 142
## 2 Thyr_Inh Thyr_Ag 6.1726199 3.098622e-07 14
## 3 Ret_Ag Thyr_Ag 10.9057151 3.063677e-40 81
## 4 Ret_Inh Thyr_Ag 0.0000000 1.000000e+00 0
## 5 Estr_Ag Thyr_Ag 24.4691632 2.641447e-65 84
## 6 Andr_Ag Thyr_Ag 533.9879643 4.435963e-10 5
## 7 Andr_Inh Thyr_Ag 0.0000000 1.000000e+00 0
## 8 GC_Ag Thyr_Ag 0.0000000 1.000000e+00 0
## 9 GC_Inh Thyr_Ag 0.0000000 1.000000e+00 0
## 10 LivX_Ag Thyr_Ag 23.6359221 4.556114e-48 56
## 11 LivX_Inh Thyr_Ag 0.0000000 1.000000e+00 0
## 12 AhHyd_Ag Thyr_Ag 0.0000000 1.000000e+00 0
## 13 AhHyd_Inh Thyr_Ag 47.2220668 5.358972e-06 4
## 14 Thyr_Ag Thyr_Inh 6.1726199 3.098622e-07 14
## 15 Thyr_Inh Thyr_Inh 1.0000000 1.000000e+00 270
## 16 Ret_Ag Thyr_Inh 3.4226795 1.283202e-16 80
## 17 Ret_Inh Thyr_Inh 0.0000000 1.000000e+00 0
## 18 Estr_Ag Thyr_Inh 2.6732328 4.298987e-07 39
## 19 Andr_Ag Thyr_Inh 27.1473236 4.707606e-03 2
## 20 Andr_Inh Thyr_Inh 0.0000000 1.000000e+00 0
## 21 GC_Ag Thyr_Inh 0.0000000 1.000000e+00 0
## 22 GC_Inh Thyr_Inh 37.9291424 3.270578e-21 19
## 23 LivX_Ag Thyr_Inh 11.4221654 2.868436e-39 64
## 24 LivX_Inh Thyr_Inh 0.0000000 1.000000e+00 0
## 25 AhHyd_Ag Thyr_Inh 0.0000000 1.000000e+00 0
## 26 AhHyd_Inh Thyr_Inh 34.3208830 2.187153e-06 5
## 27 Thyr_Ag Ret_Ag 10.9057151 3.063677e-40 81
## 28 Thyr_Inh Ret_Ag 3.4226795 1.283202e-16 80
## 29 Ret_Ag Ret_Ag 1.0000000 1.000000e+00 1677
## 30 Ret_Inh Ret_Ag 0.0000000 1.000000e+00 0
## 31 Estr_Ag Ret_Ag 10.9234073 3.762356e-212 462
## 32 Andr_Ag Ret_Ag 15.7395497 2.013961e-03 4
## 33 Andr_Inh Ret_Ag 0.0000000 1.000000e+00 0
## 34 GC_Ag Ret_Ag 1.5712909 5.128154e-01 1
## 35 GC_Inh Ret_Ag 2.9322904 2.001744e-03 13
## 36 LivX_Ag Ret_Ag 44.2014086 1.730574e-276 367
## 37 LivX_Inh Ret_Ag 0.0000000 1.000000e+00 0
## 38 AhHyd_Ag Ret_Ag 0.0000000 1.000000e+00 0
## 39 AhHyd_Inh Ret_Ag 26.3228390 6.821193e-08 10
## 40 Thyr_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 41 Thyr_Inh Ret_Inh 0.0000000 1.000000e+00 0
## 42 Ret_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 43 Ret_Inh Ret_Inh 1.0000000 1.000000e+00 1
## 44 Estr_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 45 Andr_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 46 Andr_Inh Ret_Inh 0.0000000 1.000000e+00 0
## 47 GC_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 48 GC_Inh Ret_Inh 0.0000000 1.000000e+00 0
## 49 LivX_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 50 LivX_Inh Ret_Inh 0.0000000 1.000000e+00 0
## 51 AhHyd_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 52 AhHyd_Inh Ret_Inh Inf 8.754209e-04 1
## 53 Thyr_Ag Estr_Ag 24.4691632 2.641447e-65 84
## 54 Thyr_Inh Estr_Ag 2.6732328 4.298987e-07 39
## 55 Ret_Ag Estr_Ag 10.9234073 3.762356e-212 462
## 56 Ret_Inh Estr_Ag 0.0000000 1.000000e+00 0
## 57 Estr_Ag Estr_Ag 1.0000000 1.000000e+00 905
## 58 Andr_Ag Estr_Ag 30.9435619 1.861609e-04 4
## 59 Andr_Inh Estr_Ag 0.0000000 1.000000e+00 0
## 60 GC_Ag Estr_Ag 3.0836743 3.143162e-01 1
## 61 GC_Inh Estr_Ag 0.6692207 7.992924e-01 2
## 62 LivX_Ag Estr_Ag 18.9463251 1.688829e-149 219
## 63 LivX_Inh Estr_Ag 0.0000000 1.000000e+00 0
## 64 AhHyd_Ag Estr_Ag 0.0000000 1.000000e+00 0
## 65 AhHyd_Inh Estr_Ag 24.8479088 1.805333e-07 8
## 66 Thyr_Ag Andr_Ag 533.9879643 4.435963e-10 5
## 67 Thyr_Inh Andr_Ag 27.1473236 4.707606e-03 2
## 68 Ret_Ag Andr_Ag 15.7395497 2.013961e-03 4
## 69 Ret_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 70 Estr_Ag Andr_Ag 30.9435619 1.861609e-04 4
## 71 Andr_Ag Andr_Ag 1.0000000 1.000000e+00 6
## 72 Andr_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 73 GC_Ag Andr_Ag 0.0000000 1.000000e+00 0
## 74 GC_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 75 LivX_Ag Andr_Ag 161.9107898 1.462864e-07 5
## 76 LivX_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 77 AhHyd_Ag Andr_Ag 0.0000000 1.000000e+00 0
## 78 AhHyd_Inh Andr_Ag 652.3289113 1.059093e-05 2
## 79 Thyr_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 80 Thyr_Inh Andr_Inh 0.0000000 1.000000e+00 0
## 81 Ret_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 82 Ret_Inh Andr_Inh 0.0000000 1.000000e+00 0
## 83 Estr_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 84 Andr_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 85 Andr_Inh Andr_Inh 1.0000000 1.000000e+00 1
## 86 GC_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 87 GC_Inh Andr_Inh 0.0000000 1.000000e+00 0
## 88 LivX_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 89 LivX_Inh Andr_Inh 0.0000000 1.000000e+00 0
## 90 AhHyd_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 91 AhHyd_Inh Andr_Inh 0.0000000 1.000000e+00 0
## 92 Thyr_Ag GC_Ag 0.0000000 1.000000e+00 0
## 93 Thyr_Inh GC_Ag 0.0000000 1.000000e+00 0
## 94 Ret_Ag GC_Ag 1.5712909 5.128154e-01 1
## 95 Ret_Inh GC_Ag 0.0000000 1.000000e+00 0
## 96 Estr_Ag GC_Ag 3.0836743 3.143162e-01 1
## 97 Andr_Ag GC_Ag 0.0000000 1.000000e+00 0
## 98 Andr_Inh GC_Ag 0.0000000 1.000000e+00 0
## 99 GC_Ag GC_Ag 1.0000000 1.000000e+00 6
## 100 GC_Inh GC_Ag 0.0000000 1.000000e+00 0
## 101 LivX_Ag GC_Ag 0.0000000 1.000000e+00 0
## 102 LivX_Inh GC_Ag 0.0000000 1.000000e+00 0
## 103 AhHyd_Ag GC_Ag 0.0000000 1.000000e+00 0
## 104 AhHyd_Inh GC_Ag 0.0000000 1.000000e+00 0
## 105 Thyr_Ag GC_Inh 0.0000000 1.000000e+00 0
## 106 Thyr_Inh GC_Inh 37.9291424 3.270578e-21 19
## 107 Ret_Ag GC_Inh 2.9322904 2.001744e-03 13
## 108 Ret_Inh GC_Inh 0.0000000 1.000000e+00 0
## 109 Estr_Ag GC_Inh 0.6692207 7.992924e-01 2
## 110 Andr_Ag GC_Inh 0.0000000 1.000000e+00 0
## 111 Andr_Inh GC_Inh 0.0000000 1.000000e+00 0
## 112 GC_Ag GC_Inh 0.0000000 1.000000e+00 0
## 113 GC_Inh GC_Inh 1.0000000 1.000000e+00 48
## 114 LivX_Ag GC_Inh 3.7512195 1.467358e-02 5
## 115 LivX_Inh GC_Inh 0.0000000 1.000000e+00 0
## 116 AhHyd_Ag GC_Inh 0.0000000 1.000000e+00 0
## 117 AhHyd_Inh GC_Inh 26.1977029 4.123119e-02 1
## 118 Thyr_Ag LivX_Ag 23.6359221 4.556114e-48 56
## 119 Thyr_Inh LivX_Ag 11.4221654 2.868436e-39 64
## 120 Ret_Ag LivX_Ag 44.2014086 1.730574e-276 367
## 121 Ret_Inh LivX_Ag 0.0000000 1.000000e+00 0
## 122 Estr_Ag LivX_Ag 18.9463251 1.688829e-149 219
## 123 Andr_Ag LivX_Ag 161.9107898 1.462864e-07 5
## 124 Andr_Inh LivX_Ag 0.0000000 1.000000e+00 0
## 125 GC_Ag LivX_Ag 0.0000000 1.000000e+00 0
## 126 GC_Inh LivX_Ag 3.7512195 1.467358e-02 5
## 127 LivX_Ag LivX_Ag 1.0000000 1.000000e+00 450
## 128 LivX_Inh LivX_Ag 0.0000000 1.000000e+00 0
## 129 AhHyd_Ag LivX_Ag 0.0000000 1.000000e+00 0
## 130 AhHyd_Inh LivX_Ag 108.7022748 1.560309e-13 10
## 131 Thyr_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 132 Thyr_Inh LivX_Inh 0.0000000 1.000000e+00 0
## 133 Ret_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 134 Ret_Inh LivX_Inh 0.0000000 1.000000e+00 0
## 135 Estr_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 136 Andr_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 137 Andr_Inh LivX_Inh 0.0000000 1.000000e+00 0
## 138 GC_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 139 GC_Inh LivX_Inh 0.0000000 1.000000e+00 0
## 140 LivX_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 141 LivX_Inh LivX_Inh 1.0000000 1.000000e+00 4
## 142 AhHyd_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 143 AhHyd_Inh LivX_Inh 0.0000000 1.000000e+00 0
## 144 Thyr_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 145 Thyr_Inh AhHyd_Ag 0.0000000 1.000000e+00 0
## 146 Ret_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 147 Ret_Inh AhHyd_Ag 0.0000000 1.000000e+00 0
## 148 Estr_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 149 Andr_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 150 Andr_Inh AhHyd_Ag 0.0000000 1.000000e+00 0
## 151 GC_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 152 GC_Inh AhHyd_Ag 0.0000000 1.000000e+00 0
## 153 LivX_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 154 LivX_Inh AhHyd_Ag 0.0000000 1.000000e+00 0
## 155 AhHyd_Ag AhHyd_Ag 1.0000000 1.000000e+00 3
## 156 AhHyd_Inh AhHyd_Ag 0.0000000 1.000000e+00 0
## 157 Thyr_Ag AhHyd_Inh 47.2220668 5.358972e-06 4
## 158 Thyr_Inh AhHyd_Inh 34.3208830 2.187153e-06 5
## 159 Ret_Ag AhHyd_Inh 26.3228390 6.821193e-08 10
## 160 Ret_Inh AhHyd_Inh Inf 8.754209e-04 1
## 161 Estr_Ag AhHyd_Inh 24.8479088 1.805333e-07 8
## 162 Andr_Ag AhHyd_Inh 652.3289113 1.059093e-05 2
## 163 Andr_Inh AhHyd_Inh 0.0000000 1.000000e+00 0
## 164 GC_Ag AhHyd_Inh 0.0000000 1.000000e+00 0
## 165 GC_Inh AhHyd_Inh 26.1977029 4.123119e-02 1
## 166 LivX_Ag AhHyd_Inh 108.7022748 1.560309e-13 10
## 167 LivX_Inh AhHyd_Inh 0.0000000 1.000000e+00 0
## 168 AhHyd_Ag AhHyd_Inh 0.0000000 1.000000e+00 0
## 169 AhHyd_Inh AhHyd_Inh 1.0000000 1.000000e+00 13DotPlot: visualization
I select as significant overlaps having an OR > 2 and at least 25 overlapping genes. Dots are shown for PVals < 0.01 (set in the plot). Max value in the plot must be set according to minimum PVal to avoid dots not to be shown.
cols <- viridis::cividis(100)[1:80]
ResSel <- dplyr::filter(ResMod, OR > 2) %>% dplyr::filter(Numbers > 25)
min(ResSel$Pval)## [1] 1.730574e-276max(ResSel$OR)## [1] 44.20141Dot <- ggplot(ResSel, aes(DEGs, KBase, label=Numbers)) +
geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1)) +
ggtitle('Overlap across upregulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_UpReg.pdf'), width=8, height=8)5.3 Visualize overlap results selectively for retinoic, liverX, estrogen, thyroid
Selection
Starting from already selected results, we identify only the ones related to the pathways of interest.
Path <- c('Thyr_Ag', 'Thyr_Inh', 'Ret_Ag', 'Ret_Inh', 'Estr_Ag', 'LivX_Ag', 'LivX_Inh')
ResPath <- ResSel[ResSel$DEGs %in% Path & ResSel$KBase %in% Path, ]
ResPath
## DEGs KBase OR Pval Numbers
## 1 Ret_Ag Thyr_Ag 10.905715 3.063677e-40 81
## 2 Estr_Ag Thyr_Ag 24.469163 2.641447e-65 84
## 3 LivX_Ag Thyr_Ag 23.635922 4.556114e-48 56
## 4 Ret_Ag Thyr_Inh 3.422680 1.283202e-16 80
## 5 Estr_Ag Thyr_Inh 2.673233 4.298987e-07 39
## 6 LivX_Ag Thyr_Inh 11.422165 2.868436e-39 64
## 7 Thyr_Ag Ret_Ag 10.905715 3.063677e-40 81
## 8 Thyr_Inh Ret_Ag 3.422680 1.283202e-16 80
## 9 Estr_Ag Ret_Ag 10.923407 3.762356e-212 462
## 10 LivX_Ag Ret_Ag 44.201409 1.730574e-276 367
## 11 Thyr_Ag Estr_Ag 24.469163 2.641447e-65 84
## 12 Thyr_Inh Estr_Ag 2.673233 4.298987e-07 39
## 13 Ret_Ag Estr_Ag 10.923407 3.762356e-212 462
## 14 LivX_Ag Estr_Ag 18.946325 1.688829e-149 219
## 15 Thyr_Ag LivX_Ag 23.635922 4.556114e-48 56
## 16 Thyr_Inh LivX_Ag 11.422165 2.868436e-39 64
## 17 Ret_Ag LivX_Ag 44.201409 1.730574e-276 367
## 18 Estr_Ag LivX_Ag 18.946325 1.688829e-149 219DotPlot: visualization
min(ResPath$Pval)## [1] 1.730574e-276max(ResPath$OR)## [1] 44.20141Dot <- ggplot(ResPath, aes(DEGs, KBase, label=Numbers)) +
geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1))+
ggtitle('Overlap across up-regulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_Upreg_Selected.pdf'), width=8, height=8)6. Comparison across pathways: down-regulated genes
6.1 Perform the overlap
DEGs_DownReg <- list(
Thyr_Ag= row.names(DEA$Thyr$Agonist$DEGs[DEA$Thyr$Agonist$DEGs$log2FoldChange < 0, ]),
Thyr_Inh= row.names(DEA$Thyr$Inhibitor$DEGs[DEA$Thyr$Inhibitor$DEGs$log2FoldChange < 0, ]),
Ret_Ag= row.names(DEA$Ret$Agonist$DEGs[DEA$Ret$Agonist$DEGs$log2FoldChange < 0, ]),
Ret_Inh= row.names(DEA$Ret$Inhibitor$DEGs[DEA$Ret$Inhibitor$DEGs$log2FoldChange < 0, ]),
Estr_Ag= row.names(DEA$Estr$Agonist$DEGs[DEA$Estr$Agonist$DEGs$log2FoldChange < 0, ]),
Andr_Ag= row.names(DEA$Andr$Agonist$DEGs[DEA$Andr$Agonist$DEGs$log2FoldChange < 0, ]),
Andr_Inh= row.names(DEA$Andr$Inhibitor$DEGs[DEA$Andr$Inhibitor$DEGs$log2FoldChange < 0, ]),
GC_Ag= row.names(DEA$GC$Agonist$DEGs[DEA$GC$Agonist$DEGs$log2FoldChange < 0, ]),
GC_Inh= row.names(DEA$GC$Inhibitor$DEGs[DEA$GC$Inhibitor$DEGs$log2FoldChange < 0, ]),
LivX_Ag= row.names(DEA$LivX$Agonist$DEGs[DEA$LivX$Agonist$DEGs$log2FoldChange < 0, ]),
LivX_Inh= row.names(DEA$LivX$Inhibitor$DEGs[DEA$LivX$Inhibitor$DEGs$log2FoldChange < 0, ]),
AhHyd_Ag= row.names(DEA$AhHyd$Agonist$DEGs[DEA$AhHyd$Agonist$DEGs$log2FoldChange < 0, ]),
AhHyd_Inh= row.names(DEA$AhHyd$Inhibitor$DEGs[DEA$AhHyd$Inhibitor$DEGs$log2FoldChange < 0, ])
)Universe <- row.names(DEA$Ret$Inhibitor$Res) %>% unique()
length(Universe)
## [1] 14850OvObj <- newGOM(DEGs_DownReg, DEGs_DownReg, genome.size=length(Universe))
print(OvObj)
## A GeneOverlapMatrix object:
## ###### Intersection ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Andr_Ag Andr_Inh GC_Ag GC_Inh
## Thyr_Ag 22 0 2 4 8 1 3 0 0
## Thyr_Inh 0 188 92 1 18 0 0 0 65
## Ret_Ag 2 92 1369 2 401 1 0 0 61
## Ret_Inh 4 1 2 7 3 2 1 0 1
## Estr_Ag 8 18 401 3 797 2 1 1 14
## Andr_Ag 1 0 1 2 2 4 0 0 0
## Andr_Inh 3 0 0 1 1 0 8 0 1
## GC_Ag 0 0 0 0 1 0 0 3 0
## GC_Inh 0 65 61 1 14 0 1 0 303
## LivX_Ag 0 123 210 1 72 1 1 1 68
## LivX_Inh 6 4 6 6 6 2 3 0 10
## AhHyd_Ag 12 0 2 2 9 1 3 0 1
## AhHyd_Inh 0 8 17 0 10 1 0 0 3
## LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 0 6 12 0
## Thyr_Inh 123 4 0 8
## Ret_Ag 210 6 2 17
## Ret_Inh 1 6 2 0
## Estr_Ag 72 6 9 10
## Andr_Ag 1 2 1 1
## Andr_Inh 1 3 3 0
## GC_Ag 1 0 0 0
## GC_Inh 68 10 1 3
## LivX_Ag 383 15 1 17
## LivX_Inh 15 42 3 2
## AhHyd_Ag 1 3 58 1
## AhHyd_Inh 17 2 1 29
## ###### P-value ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag
## Thyr_Ag 1.903459e-71 1.000000e+00 6.150185e-01 1.260372e-10 1.083997e-05
## Thyr_Inh 1.000000e+00 0.000000e+00 1.296458e-45 8.534049e-02 1.246963e-02
## Ret_Ag 6.150185e-01 1.296458e-45 0.000000e+00 1.306392e-01 1.370389e-215
## Ret_Inh 1.260372e-10 8.534049e-02 1.306392e-01 3.169273e-26 4.580383e-03
## Estr_Ag 1.083997e-05 1.246963e-02 1.370389e-215 4.580383e-03 0.000000e+00
## Andr_Ag 5.913366e-03 1.000000e+00 3.208514e-01 1.142304e-06 1.605467e-02
## Andr_Inh 1.572835e-07 1.000000e+00 1.000000e+00 3.765714e-03 3.568766e-01
## GC_Ag 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.525330e-01
## GC_Inh 1.000000e+00 3.521227e-63 3.519149e-09 1.344023e-01 7.558552e-01
## LivX_Ag 1.000000e+00 1.464476e-154 6.406226e-118 1.671862e-01 3.359345e-21
## LivX_Inh 2.544346e-11 1.912469e-03 1.863785e-01 2.462733e-15 2.361772e-02
## AhHyd_Ag 2.344408e-24 1.000000e+00 9.749612e-01 3.109100e-04 3.526989e-03
## AhHyd_Inh 1.000000e+00 1.943615e-09 4.044052e-11 1.000000e+00 1.477041e-06
## Andr_Ag Andr_Inh GC_Ag GC_Inh LivX_Ag
## Thyr_Ag 5.913366e-03 1.572835e-07 1.000000e+00 1.000000e+00 1.000000e+00
## Thyr_Inh 1.000000e+00 1.000000e+00 1.000000e+00 3.521227e-63 1.464476e-154
## Ret_Ag 3.208514e-01 1.000000e+00 1.000000e+00 3.519149e-09 6.406226e-118
## Ret_Inh 1.142304e-06 3.765714e-03 1.000000e+00 1.344023e-01 1.671862e-01
## Estr_Ag 1.605467e-02 3.568766e-01 1.525330e-01 7.558552e-01 3.359345e-21
## Andr_Ag 4.937202e-16 1.000000e+00 1.000000e+00 1.000000e+00 9.925167e-02
## Andr_Inh 1.000000e+00 1.708157e-29 1.000000e+00 1.520723e-01 1.886756e-01
## GC_Ag 1.000000e+00 1.000000e+00 1.832566e-12 1.000000e+00 7.540027e-02
## GC_Inh 1.000000e+00 1.520723e-01 1.000000e+00 0.000000e+00 8.311940e-45
## LivX_Ag 9.925167e-02 1.886756e-01 7.540027e-02 8.311940e-45 0.000000e+00
## LivX_Inh 4.668738e-05 1.166562e-06 1.000000e+00 8.906368e-09 5.928677e-14
## AhHyd_Ag 1.553317e-02 3.122823e-06 1.000000e+00 6.982025e-01 7.809545e-01
## AhHyd_Inh 7.789380e-03 1.000000e+00 1.000000e+00 2.077014e-02 2.721352e-20
## LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 2.544346e-11 2.344408e-24 1.000000e+00
## Thyr_Inh 1.912469e-03 1.000000e+00 1.943615e-09
## Ret_Ag 1.863785e-01 9.749612e-01 4.044052e-11
## Ret_Inh 2.462733e-15 3.109100e-04 1.000000e+00
## Estr_Ag 2.361772e-02 3.526989e-03 1.477041e-06
## Andr_Ag 4.668738e-05 1.553317e-02 7.789380e-03
## Andr_Inh 1.166562e-06 3.122823e-06 1.000000e+00
## GC_Ag 1.000000e+00 1.000000e+00 1.000000e+00
## GC_Inh 8.906368e-09 6.982025e-01 2.077014e-02
## LivX_Ag 5.928677e-14 7.809545e-01 2.721352e-20
## LivX_Inh 9.127902e-125 5.825559e-04 3.020683e-03
## AhHyd_Ag 5.825559e-04 2.880331e-164 1.073807e-01
## AhHyd_Inh 3.020683e-03 1.073807e-01 9.513776e-91
## ###### Odds Ratio ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Andr_Ag
## Thyr_Ag Inf 0.000000 0.9847119 1072.559553 10.1637020 233.878672
## Thyr_Inh 0.0000000 Inf 10.0416079 13.053133 1.8869453 0.000000
## Ret_Ag 0.9847119 10.041608 Inf 3.942233 13.6832853 3.283691
## Ret_Inh 1072.5595526 13.053133 3.9422335 Inf 13.2688496 2628.731552
## Estr_Ag 10.1637020 1.886945 13.6832853 13.268850 Inf 17.661478
## Andr_Ag 233.8786721 0.000000 3.2836910 2628.731552 17.6614783 Inf
## Andr_Inh 457.8089118 0.000000 0.0000000 347.875457 2.5205522 0.000000
## GC_Ag 0.0000000 0.000000 0.0000000 0.000000 8.8236122 0.000000
## GC_Inh 0.0000000 31.989423 2.5510737 8.021994 0.8515592 0.000000
## LivX_Ag 0.0000000 104.389398 13.9349772 6.307319 4.3873765 12.611124
## LivX_Inh 153.6352357 8.362407 1.6439679 2421.329155 2.9530719 364.113328
## AhHyd_Ag 380.7075634 0.000000 0.3507583 104.966944 3.2637058 86.109402
## AhHyd_Inh 0.0000000 30.931807 14.1076574 0.000000 9.3823040 174.829143
## Andr_Inh GC_Ag GC_Inh LivX_Ag LivX_Inh AhHyd_Ag
## Thyr_Ag 457.808912 0.000000 0.0000000 0.0000000 153.635236 380.7075634
## Thyr_Inh 0.000000 0.000000 31.9894230 104.3893984 8.362407 0.0000000
## Ret_Ag 0.000000 0.000000 2.5510737 13.9349772 1.643968 0.3507583
## Ret_Inh 347.875457 0.000000 8.0219944 6.3073195 2421.329155 104.9669442
## Estr_Ag 2.520552 8.823612 0.8515592 4.3873765 2.953072 3.2637058
## Andr_Ag 0.000000 0.000000 0.0000000 12.6111237 364.113328 86.1094022
## Andr_Inh Inf 0.000000 6.8754749 5.4058483 224.966301 160.2681655
## GC_Ag 0.000000 Inf 0.0000000 18.9188897 0.000000 0.0000000
## GC_Inh 6.875475 0.000000 Inf 13.0654542 15.473027 0.8417655
## LivX_Ag 5.405848 18.918890 13.0654542 Inf 21.780016 0.6618125
## LivX_Inh 224.966301 0.000000 15.4730269 21.7800158 Inf 20.6081686
## AhHyd_Ag 160.268166 0.000000 0.8417655 0.6618125 20.608169 Inf
## AhHyd_Inh 0.000000 0.000000 5.5834179 55.8396611 27.338048 9.2478668
## AhHyd_Inh
## Thyr_Ag 0.000000
## Thyr_Inh 30.931807
## Ret_Ag 14.107657
## Ret_Inh 0.000000
## Estr_Ag 9.382304
## Andr_Ag 174.829143
## Andr_Inh 0.000000
## GC_Ag 0.000000
## GC_Inh 5.583418
## LivX_Ag 55.839661
## LivX_Inh 27.338048
## AhHyd_Ag 9.247867
## AhHyd_Inh Inf
## ###### Jaccard Index ######
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag
## Thyr_Ag 1.000000000 0.000000000 0.001439885 0.160000000 0.009864365
## Thyr_Inh 0.000000000 1.000000000 0.062798635 0.005154639 0.018614271
## Ret_Ag 0.001439885 0.062798635 1.000000000 0.001455604 0.227195467
## Ret_Inh 0.160000000 0.005154639 0.001455604 1.000000000 0.003745318
## Estr_Ag 0.009864365 0.018614271 0.227195467 0.003745318 1.000000000
## Andr_Ag 0.040000000 0.000000000 0.000728863 0.222222222 0.002503129
## Andr_Inh 0.111111111 0.000000000 0.000000000 0.071428571 0.001243781
## GC_Ag 0.000000000 0.000000000 0.000000000 0.000000000 0.001251564
## GC_Inh 0.000000000 0.152582160 0.037864680 0.003236246 0.012891344
## LivX_Ag 0.000000000 0.274553571 0.136186770 0.002570694 0.064981949
## LivX_Inh 0.103448276 0.017699115 0.004270463 0.139534884 0.007202881
## AhHyd_Ag 0.176470588 0.000000000 0.001403509 0.031746032 0.010638298
## AhHyd_Inh 0.000000000 0.038277512 0.012309920 0.000000000 0.012254902
## Andr_Ag Andr_Inh GC_Ag GC_Inh LivX_Ag
## Thyr_Ag 0.040000000 0.111111111 0.000000000 0.000000000 0.000000000
## Thyr_Inh 0.000000000 0.000000000 0.000000000 0.152582160 0.274553571
## Ret_Ag 0.000728863 0.000000000 0.000000000 0.037864680 0.136186770
## Ret_Inh 0.222222222 0.071428571 0.000000000 0.003236246 0.002570694
## Estr_Ag 0.002503129 0.001243781 0.001251564 0.012891344 0.064981949
## Andr_Ag 1.000000000 0.000000000 0.000000000 0.000000000 0.002590674
## Andr_Inh 0.000000000 1.000000000 0.000000000 0.003225806 0.002564103
## GC_Ag 0.000000000 0.000000000 1.000000000 0.000000000 0.002597403
## GC_Inh 0.000000000 0.003225806 0.000000000 1.000000000 0.110032362
## LivX_Ag 0.002590674 0.002564103 0.002597403 0.110032362 1.000000000
## LivX_Inh 0.045454545 0.063829787 0.000000000 0.029850746 0.036585366
## AhHyd_Ag 0.016393443 0.047619048 0.000000000 0.002777778 0.002272727
## AhHyd_Inh 0.031250000 0.000000000 0.000000000 0.009118541 0.043037975
## LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 0.103448276 0.176470588 0.000000000
## Thyr_Inh 0.017699115 0.000000000 0.038277512
## Ret_Ag 0.004270463 0.001403509 0.012309920
## Ret_Inh 0.139534884 0.031746032 0.000000000
## Estr_Ag 0.007202881 0.010638298 0.012254902
## Andr_Ag 0.045454545 0.016393443 0.031250000
## Andr_Inh 0.063829787 0.047619048 0.000000000
## GC_Ag 0.000000000 0.000000000 0.000000000
## GC_Inh 0.029850746 0.002777778 0.009118541
## LivX_Ag 0.036585366 0.002272727 0.043037975
## LivX_Inh 1.000000000 0.030927835 0.028985507
## AhHyd_Ag 0.030927835 1.000000000 0.011627907
## AhHyd_Inh 0.028985507 0.011627907 1.000000000getMatrix(OvObj, name='intersection')
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Andr_Ag Andr_Inh GC_Ag GC_Inh
## Thyr_Ag 22 0 2 4 8 1 3 0 0
## Thyr_Inh 0 188 92 1 18 0 0 0 65
## Ret_Ag 2 92 1369 2 401 1 0 0 61
## Ret_Inh 4 1 2 7 3 2 1 0 1
## Estr_Ag 8 18 401 3 797 2 1 1 14
## Andr_Ag 1 0 1 2 2 4 0 0 0
## Andr_Inh 3 0 0 1 1 0 8 0 1
## GC_Ag 0 0 0 0 1 0 0 3 0
## GC_Inh 0 65 61 1 14 0 1 0 303
## LivX_Ag 0 123 210 1 72 1 1 1 68
## LivX_Inh 6 4 6 6 6 2 3 0 10
## AhHyd_Ag 12 0 2 2 9 1 3 0 1
## AhHyd_Inh 0 8 17 0 10 1 0 0 3
## LivX_Ag LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 0 6 12 0
## Thyr_Inh 123 4 0 8
## Ret_Ag 210 6 2 17
## Ret_Inh 1 6 2 0
## Estr_Ag 72 6 9 10
## Andr_Ag 1 2 1 1
## Andr_Inh 1 3 3 0
## GC_Ag 1 0 0 0
## GC_Inh 68 10 1 3
## LivX_Ag 383 15 1 17
## LivX_Inh 15 42 3 2
## AhHyd_Ag 1 3 58 1
## AhHyd_Inh 17 2 1 29getMatrix(OvObj, name='pval')
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag
## Thyr_Ag 1.903459e-71 1.000000e+00 6.150185e-01 1.260372e-10 1.083997e-05
## Thyr_Inh 1.000000e+00 0.000000e+00 1.296458e-45 8.534049e-02 1.246963e-02
## Ret_Ag 6.150185e-01 1.296458e-45 0.000000e+00 1.306392e-01 1.370389e-215
## Ret_Inh 1.260372e-10 8.534049e-02 1.306392e-01 3.169273e-26 4.580383e-03
## Estr_Ag 1.083997e-05 1.246963e-02 1.370389e-215 4.580383e-03 0.000000e+00
## Andr_Ag 5.913366e-03 1.000000e+00 3.208514e-01 1.142304e-06 1.605467e-02
## Andr_Inh 1.572835e-07 1.000000e+00 1.000000e+00 3.765714e-03 3.568766e-01
## GC_Ag 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00 1.525330e-01
## GC_Inh 1.000000e+00 3.521227e-63 3.519149e-09 1.344023e-01 7.558552e-01
## LivX_Ag 1.000000e+00 1.464476e-154 6.406226e-118 1.671862e-01 3.359345e-21
## LivX_Inh 2.544346e-11 1.912469e-03 1.863785e-01 2.462733e-15 2.361772e-02
## AhHyd_Ag 2.344408e-24 1.000000e+00 9.749612e-01 3.109100e-04 3.526989e-03
## AhHyd_Inh 1.000000e+00 1.943615e-09 4.044052e-11 1.000000e+00 1.477041e-06
## Andr_Ag Andr_Inh GC_Ag GC_Inh LivX_Ag
## Thyr_Ag 5.913366e-03 1.572835e-07 1.000000e+00 1.000000e+00 1.000000e+00
## Thyr_Inh 1.000000e+00 1.000000e+00 1.000000e+00 3.521227e-63 1.464476e-154
## Ret_Ag 3.208514e-01 1.000000e+00 1.000000e+00 3.519149e-09 6.406226e-118
## Ret_Inh 1.142304e-06 3.765714e-03 1.000000e+00 1.344023e-01 1.671862e-01
## Estr_Ag 1.605467e-02 3.568766e-01 1.525330e-01 7.558552e-01 3.359345e-21
## Andr_Ag 4.937202e-16 1.000000e+00 1.000000e+00 1.000000e+00 9.925167e-02
## Andr_Inh 1.000000e+00 1.708157e-29 1.000000e+00 1.520723e-01 1.886756e-01
## GC_Ag 1.000000e+00 1.000000e+00 1.832566e-12 1.000000e+00 7.540027e-02
## GC_Inh 1.000000e+00 1.520723e-01 1.000000e+00 0.000000e+00 8.311940e-45
## LivX_Ag 9.925167e-02 1.886756e-01 7.540027e-02 8.311940e-45 0.000000e+00
## LivX_Inh 4.668738e-05 1.166562e-06 1.000000e+00 8.906368e-09 5.928677e-14
## AhHyd_Ag 1.553317e-02 3.122823e-06 1.000000e+00 6.982025e-01 7.809545e-01
## AhHyd_Inh 7.789380e-03 1.000000e+00 1.000000e+00 2.077014e-02 2.721352e-20
## LivX_Inh AhHyd_Ag AhHyd_Inh
## Thyr_Ag 2.544346e-11 2.344408e-24 1.000000e+00
## Thyr_Inh 1.912469e-03 1.000000e+00 1.943615e-09
## Ret_Ag 1.863785e-01 9.749612e-01 4.044052e-11
## Ret_Inh 2.462733e-15 3.109100e-04 1.000000e+00
## Estr_Ag 2.361772e-02 3.526989e-03 1.477041e-06
## Andr_Ag 4.668738e-05 1.553317e-02 7.789380e-03
## Andr_Inh 1.166562e-06 3.122823e-06 1.000000e+00
## GC_Ag 1.000000e+00 1.000000e+00 1.000000e+00
## GC_Inh 8.906368e-09 6.982025e-01 2.077014e-02
## LivX_Ag 5.928677e-14 7.809545e-01 2.721352e-20
## LivX_Inh 9.127902e-125 5.825559e-04 3.020683e-03
## AhHyd_Ag 5.825559e-04 2.880331e-164 1.073807e-01
## AhHyd_Inh 3.020683e-03 1.073807e-01 9.513776e-91getMatrix(OvObj, name='odds.ratio')
## Thyr_Ag Thyr_Inh Ret_Ag Ret_Inh Estr_Ag Andr_Ag
## Thyr_Ag Inf 0.000000 0.9847119 1072.559553 10.1637020 233.878672
## Thyr_Inh 0.0000000 Inf 10.0416079 13.053133 1.8869453 0.000000
## Ret_Ag 0.9847119 10.041608 Inf 3.942233 13.6832853 3.283691
## Ret_Inh 1072.5595526 13.053133 3.9422335 Inf 13.2688496 2628.731552
## Estr_Ag 10.1637020 1.886945 13.6832853 13.268850 Inf 17.661478
## Andr_Ag 233.8786721 0.000000 3.2836910 2628.731552 17.6614783 Inf
## Andr_Inh 457.8089118 0.000000 0.0000000 347.875457 2.5205522 0.000000
## GC_Ag 0.0000000 0.000000 0.0000000 0.000000 8.8236122 0.000000
## GC_Inh 0.0000000 31.989423 2.5510737 8.021994 0.8515592 0.000000
## LivX_Ag 0.0000000 104.389398 13.9349772 6.307319 4.3873765 12.611124
## LivX_Inh 153.6352357 8.362407 1.6439679 2421.329155 2.9530719 364.113328
## AhHyd_Ag 380.7075634 0.000000 0.3507583 104.966944 3.2637058 86.109402
## AhHyd_Inh 0.0000000 30.931807 14.1076574 0.000000 9.3823040 174.829143
## Andr_Inh GC_Ag GC_Inh LivX_Ag LivX_Inh AhHyd_Ag
## Thyr_Ag 457.808912 0.000000 0.0000000 0.0000000 153.635236 380.7075634
## Thyr_Inh 0.000000 0.000000 31.9894230 104.3893984 8.362407 0.0000000
## Ret_Ag 0.000000 0.000000 2.5510737 13.9349772 1.643968 0.3507583
## Ret_Inh 347.875457 0.000000 8.0219944 6.3073195 2421.329155 104.9669442
## Estr_Ag 2.520552 8.823612 0.8515592 4.3873765 2.953072 3.2637058
## Andr_Ag 0.000000 0.000000 0.0000000 12.6111237 364.113328 86.1094022
## Andr_Inh Inf 0.000000 6.8754749 5.4058483 224.966301 160.2681655
## GC_Ag 0.000000 Inf 0.0000000 18.9188897 0.000000 0.0000000
## GC_Inh 6.875475 0.000000 Inf 13.0654542 15.473027 0.8417655
## LivX_Ag 5.405848 18.918890 13.0654542 Inf 21.780016 0.6618125
## LivX_Inh 224.966301 0.000000 15.4730269 21.7800158 Inf 20.6081686
## AhHyd_Ag 160.268166 0.000000 0.8417655 0.6618125 20.608169 Inf
## AhHyd_Inh 0.000000 0.000000 5.5834179 55.8396611 27.338048 9.2478668
## AhHyd_Inh
## Thyr_Ag 0.000000
## Thyr_Inh 30.931807
## Ret_Ag 14.107657
## Ret_Inh 0.000000
## Estr_Ag 9.382304
## Andr_Ag 174.829143
## Andr_Inh 0.000000
## GC_Ag 0.000000
## GC_Inh 5.583418
## LivX_Ag 55.839661
## LivX_Inh 27.338048
## AhHyd_Ag 9.247867
## AhHyd_Inh Inf6.2 Visualize overlap results
DotPlot: data preparation
OR <- data.frame(getMatrix(OvObj, name='odds.ratio'))
OR$DEGs <- row.names(OR)
OR <- gather(OR, 'KBase', 'OR', -DEGs)
PVAL <- data.frame(getMatrix(OvObj, name='pval'))
PVAL$DEGs <- row.names(PVAL)
PVAL <- gather(PVAL, 'KBase', 'PVal', -DEGs)
NUM <- data.frame(getMatrix(OvObj, name='intersection'))
NUM$DEGs <- row.names(NUM)
NUM <- gather(NUM, 'KBase', 'Numbers', -DEGs)
if(! identical(OR$DEGs, PVAL$DEGs)){
stop('Inconsistecy')
}
if(! identical(OR$DEGs, NUM$DEGs)){
stop('Inconsistecy')
}
if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}
if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}
Res <- mutate(OR, Pval=PVAL$PVal) %>% mutate(Numbers=NUM$Numbers)
Res
## DEGs KBase OR Pval Numbers
## 1 Thyr_Ag Thyr_Ag Inf 1.903459e-71 22
## 2 Thyr_Inh Thyr_Ag 0.0000000 1.000000e+00 0
## 3 Ret_Ag Thyr_Ag 0.9847119 6.150185e-01 2
## 4 Ret_Inh Thyr_Ag 1072.5595526 1.260372e-10 4
## 5 Estr_Ag Thyr_Ag 10.1637020 1.083997e-05 8
## 6 Andr_Ag Thyr_Ag 233.8786721 5.913366e-03 1
## 7 Andr_Inh Thyr_Ag 457.8089118 1.572835e-07 3
## 8 GC_Ag Thyr_Ag 0.0000000 1.000000e+00 0
## 9 GC_Inh Thyr_Ag 0.0000000 1.000000e+00 0
## 10 LivX_Ag Thyr_Ag 0.0000000 1.000000e+00 0
## 11 LivX_Inh Thyr_Ag 153.6352357 2.544346e-11 6
## 12 AhHyd_Ag Thyr_Ag 380.7075634 2.344408e-24 12
## 13 AhHyd_Inh Thyr_Ag 0.0000000 1.000000e+00 0
## 14 Thyr_Ag Thyr_Inh 0.0000000 1.000000e+00 0
## 15 Thyr_Inh Thyr_Inh Inf 0.000000e+00 188
## 16 Ret_Ag Thyr_Inh 10.0416079 1.296458e-45 92
## 17 Ret_Inh Thyr_Inh 13.0531334 8.534049e-02 1
## 18 Estr_Ag Thyr_Inh 1.8869453 1.246963e-02 18
## 19 Andr_Ag Thyr_Inh 0.0000000 1.000000e+00 0
## 20 Andr_Inh Thyr_Inh 0.0000000 1.000000e+00 0
## 21 GC_Ag Thyr_Inh 0.0000000 1.000000e+00 0
## 22 GC_Inh Thyr_Inh 31.9894230 3.521227e-63 65
## 23 LivX_Ag Thyr_Inh 104.3893984 1.464476e-154 123
## 24 LivX_Inh Thyr_Inh 8.3624069 1.912469e-03 4
## 25 AhHyd_Ag Thyr_Inh 0.0000000 1.000000e+00 0
## 26 AhHyd_Inh Thyr_Inh 30.9318073 1.943615e-09 8
## 27 Thyr_Ag Ret_Ag 0.9847119 6.150185e-01 2
## 28 Thyr_Inh Ret_Ag 10.0416079 1.296458e-45 92
## 29 Ret_Ag Ret_Ag Inf 0.000000e+00 1369
## 30 Ret_Inh Ret_Ag 3.9422335 1.306392e-01 2
## 31 Estr_Ag Ret_Ag 13.6832853 1.370389e-215 401
## 32 Andr_Ag Ret_Ag 3.2836910 3.208514e-01 1
## 33 Andr_Inh Ret_Ag 0.0000000 1.000000e+00 0
## 34 GC_Ag Ret_Ag 0.0000000 1.000000e+00 0
## 35 GC_Inh Ret_Ag 2.5510737 3.519149e-09 61
## 36 LivX_Ag Ret_Ag 13.9349772 6.406226e-118 210
## 37 LivX_Inh Ret_Ag 1.6439679 1.863785e-01 6
## 38 AhHyd_Ag Ret_Ag 0.3507583 9.749612e-01 2
## 39 AhHyd_Inh Ret_Ag 14.1076574 4.044052e-11 17
## 40 Thyr_Ag Ret_Inh 1072.5595526 1.260372e-10 4
## 41 Thyr_Inh Ret_Inh 13.0531334 8.534049e-02 1
## 42 Ret_Ag Ret_Inh 3.9422335 1.306392e-01 2
## 43 Ret_Inh Ret_Inh Inf 3.169273e-26 7
## 44 Estr_Ag Ret_Inh 13.2688496 4.580383e-03 3
## 45 Andr_Ag Ret_Inh 2628.7315517 1.142304e-06 2
## 46 Andr_Inh Ret_Inh 347.8754566 3.765714e-03 1
## 47 GC_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 48 GC_Inh Ret_Inh 8.0219944 1.344023e-01 1
## 49 LivX_Ag Ret_Inh 6.3073195 1.671862e-01 1
## 50 LivX_Inh Ret_Inh 2421.3291551 2.462733e-15 6
## 51 AhHyd_Ag Ret_Inh 104.9669442 3.109100e-04 2
## 52 AhHyd_Inh Ret_Inh 0.0000000 1.000000e+00 0
## 53 Thyr_Ag Estr_Ag 10.1637020 1.083997e-05 8
## 54 Thyr_Inh Estr_Ag 1.8869453 1.246963e-02 18
## 55 Ret_Ag Estr_Ag 13.6832853 1.370389e-215 401
## 56 Ret_Inh Estr_Ag 13.2688496 4.580383e-03 3
## 57 Estr_Ag Estr_Ag Inf 0.000000e+00 797
## 58 Andr_Ag Estr_Ag 17.6614783 1.605467e-02 2
## 59 Andr_Inh Estr_Ag 2.5205522 3.568766e-01 1
## 60 GC_Ag Estr_Ag 8.8236122 1.525330e-01 1
## 61 GC_Inh Estr_Ag 0.8515592 7.558552e-01 14
## 62 LivX_Ag Estr_Ag 4.3873765 3.359345e-21 72
## 63 LivX_Inh Estr_Ag 2.9530719 2.361772e-02 6
## 64 AhHyd_Ag Estr_Ag 3.2637058 3.526989e-03 9
## 65 AhHyd_Inh Estr_Ag 9.3823040 1.477041e-06 10
## 66 Thyr_Ag Andr_Ag 233.8786721 5.913366e-03 1
## 67 Thyr_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 68 Ret_Ag Andr_Ag 3.2836910 3.208514e-01 1
## 69 Ret_Inh Andr_Ag 2628.7315517 1.142304e-06 2
## 70 Estr_Ag Andr_Ag 17.6614783 1.605467e-02 2
## 71 Andr_Ag Andr_Ag Inf 4.937202e-16 4
## 72 Andr_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 73 GC_Ag Andr_Ag 0.0000000 1.000000e+00 0
## 74 GC_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 75 LivX_Ag Andr_Ag 12.6111237 9.925167e-02 1
## 76 LivX_Inh Andr_Ag 364.1133279 4.668738e-05 2
## 77 AhHyd_Ag Andr_Ag 86.1094022 1.553317e-02 1
## 78 AhHyd_Inh Andr_Ag 174.8291431 7.789380e-03 1
## 79 Thyr_Ag Andr_Inh 457.8089118 1.572835e-07 3
## 80 Thyr_Inh Andr_Inh 0.0000000 1.000000e+00 0
## 81 Ret_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 82 Ret_Inh Andr_Inh 347.8754566 3.765714e-03 1
## 83 Estr_Ag Andr_Inh 2.5205522 3.568766e-01 1
## 84 Andr_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 85 Andr_Inh Andr_Inh Inf 1.708157e-29 8
## 86 GC_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 87 GC_Inh Andr_Inh 6.8754749 1.520723e-01 1
## 88 LivX_Ag Andr_Inh 5.4058483 1.886756e-01 1
## 89 LivX_Inh Andr_Inh 224.9663006 1.166562e-06 3
## 90 AhHyd_Ag Andr_Inh 160.2681655 3.122823e-06 3
## 91 AhHyd_Inh Andr_Inh 0.0000000 1.000000e+00 0
## 92 Thyr_Ag GC_Ag 0.0000000 1.000000e+00 0
## 93 Thyr_Inh GC_Ag 0.0000000 1.000000e+00 0
## 94 Ret_Ag GC_Ag 0.0000000 1.000000e+00 0
## 95 Ret_Inh GC_Ag 0.0000000 1.000000e+00 0
## 96 Estr_Ag GC_Ag 8.8236122 1.525330e-01 1
## 97 Andr_Ag GC_Ag 0.0000000 1.000000e+00 0
## 98 Andr_Inh GC_Ag 0.0000000 1.000000e+00 0
## 99 GC_Ag GC_Ag Inf 1.832566e-12 3
## 100 GC_Inh GC_Ag 0.0000000 1.000000e+00 0
## 101 LivX_Ag GC_Ag 18.9188897 7.540027e-02 1
## 102 LivX_Inh GC_Ag 0.0000000 1.000000e+00 0
## 103 AhHyd_Ag GC_Ag 0.0000000 1.000000e+00 0
## 104 AhHyd_Inh GC_Ag 0.0000000 1.000000e+00 0
## 105 Thyr_Ag GC_Inh 0.0000000 1.000000e+00 0
## 106 Thyr_Inh GC_Inh 31.9894230 3.521227e-63 65
## 107 Ret_Ag GC_Inh 2.5510737 3.519149e-09 61
## 108 Ret_Inh GC_Inh 8.0219944 1.344023e-01 1
## 109 Estr_Ag GC_Inh 0.8515592 7.558552e-01 14
## 110 Andr_Ag GC_Inh 0.0000000 1.000000e+00 0
## 111 Andr_Inh GC_Inh 6.8754749 1.520723e-01 1
## 112 GC_Ag GC_Inh 0.0000000 1.000000e+00 0
## 113 GC_Inh GC_Inh Inf 0.000000e+00 303
## 114 LivX_Ag GC_Inh 13.0654542 8.311940e-45 68
## 115 LivX_Inh GC_Inh 15.4730269 8.906368e-09 10
## 116 AhHyd_Ag GC_Inh 0.8417655 6.982025e-01 1
## 117 AhHyd_Inh GC_Inh 5.5834179 2.077014e-02 3
## 118 Thyr_Ag LivX_Ag 0.0000000 1.000000e+00 0
## 119 Thyr_Inh LivX_Ag 104.3893984 1.464476e-154 123
## 120 Ret_Ag LivX_Ag 13.9349772 6.406226e-118 210
## 121 Ret_Inh LivX_Ag 6.3073195 1.671862e-01 1
## 122 Estr_Ag LivX_Ag 4.3873765 3.359345e-21 72
## 123 Andr_Ag LivX_Ag 12.6111237 9.925167e-02 1
## 124 Andr_Inh LivX_Ag 5.4058483 1.886756e-01 1
## 125 GC_Ag LivX_Ag 18.9188897 7.540027e-02 1
## 126 GC_Inh LivX_Ag 13.0654542 8.311940e-45 68
## 127 LivX_Ag LivX_Ag Inf 0.000000e+00 383
## 128 LivX_Inh LivX_Ag 21.7800158 5.928677e-14 15
## 129 AhHyd_Ag LivX_Ag 0.6618125 7.809545e-01 1
## 130 AhHyd_Inh LivX_Ag 55.8396611 2.721352e-20 17
## 131 Thyr_Ag LivX_Inh 153.6352357 2.544346e-11 6
## 132 Thyr_Inh LivX_Inh 8.3624069 1.912469e-03 4
## 133 Ret_Ag LivX_Inh 1.6439679 1.863785e-01 6
## 134 Ret_Inh LivX_Inh 2421.3291551 2.462733e-15 6
## 135 Estr_Ag LivX_Inh 2.9530719 2.361772e-02 6
## 136 Andr_Ag LivX_Inh 364.1133279 4.668738e-05 2
## 137 Andr_Inh LivX_Inh 224.9663006 1.166562e-06 3
## 138 GC_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 139 GC_Inh LivX_Inh 15.4730269 8.906368e-09 10
## 140 LivX_Ag LivX_Inh 21.7800158 5.928677e-14 15
## 141 LivX_Inh LivX_Inh Inf 9.127902e-125 42
## 142 AhHyd_Ag LivX_Inh 20.6081686 5.825559e-04 3
## 143 AhHyd_Inh LivX_Inh 27.3380477 3.020683e-03 2
## 144 Thyr_Ag AhHyd_Ag 380.7075634 2.344408e-24 12
## 145 Thyr_Inh AhHyd_Ag 0.0000000 1.000000e+00 0
## 146 Ret_Ag AhHyd_Ag 0.3507583 9.749612e-01 2
## 147 Ret_Inh AhHyd_Ag 104.9669442 3.109100e-04 2
## 148 Estr_Ag AhHyd_Ag 3.2637058 3.526989e-03 9
## 149 Andr_Ag AhHyd_Ag 86.1094022 1.553317e-02 1
## 150 Andr_Inh AhHyd_Ag 160.2681655 3.122823e-06 3
## 151 GC_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 152 GC_Inh AhHyd_Ag 0.8417655 6.982025e-01 1
## 153 LivX_Ag AhHyd_Ag 0.6618125 7.809545e-01 1
## 154 LivX_Inh AhHyd_Ag 20.6081686 5.825559e-04 3
## 155 AhHyd_Ag AhHyd_Ag Inf 2.880331e-164 58
## 156 AhHyd_Inh AhHyd_Ag 9.2478668 1.073807e-01 1
## 157 Thyr_Ag AhHyd_Inh 0.0000000 1.000000e+00 0
## 158 Thyr_Inh AhHyd_Inh 30.9318073 1.943615e-09 8
## 159 Ret_Ag AhHyd_Inh 14.1076574 4.044052e-11 17
## 160 Ret_Inh AhHyd_Inh 0.0000000 1.000000e+00 0
## 161 Estr_Ag AhHyd_Inh 9.3823040 1.477041e-06 10
## 162 Andr_Ag AhHyd_Inh 174.8291431 7.789380e-03 1
## 163 Andr_Inh AhHyd_Inh 0.0000000 1.000000e+00 0
## 164 GC_Ag AhHyd_Inh 0.0000000 1.000000e+00 0
## 165 GC_Inh AhHyd_Inh 5.5834179 2.077014e-02 3
## 166 LivX_Ag AhHyd_Inh 55.8396611 2.721352e-20 17
## 167 LivX_Inh AhHyd_Inh 27.3380477 3.020683e-03 2
## 168 AhHyd_Ag AhHyd_Inh 9.2478668 1.073807e-01 1
## 169 AhHyd_Inh AhHyd_Inh Inf 9.513776e-91 29ResMod <- Res
ResMod[ResMod$DEGs == ResMod$KBase, ]$OR <- 1
ResMod[ResMod$DEGs == ResMod$KBase, ]$Pval <- 1
ResMod
## DEGs KBase OR Pval Numbers
## 1 Thyr_Ag Thyr_Ag 1.0000000 1.000000e+00 22
## 2 Thyr_Inh Thyr_Ag 0.0000000 1.000000e+00 0
## 3 Ret_Ag Thyr_Ag 0.9847119 6.150185e-01 2
## 4 Ret_Inh Thyr_Ag 1072.5595526 1.260372e-10 4
## 5 Estr_Ag Thyr_Ag 10.1637020 1.083997e-05 8
## 6 Andr_Ag Thyr_Ag 233.8786721 5.913366e-03 1
## 7 Andr_Inh Thyr_Ag 457.8089118 1.572835e-07 3
## 8 GC_Ag Thyr_Ag 0.0000000 1.000000e+00 0
## 9 GC_Inh Thyr_Ag 0.0000000 1.000000e+00 0
## 10 LivX_Ag Thyr_Ag 0.0000000 1.000000e+00 0
## 11 LivX_Inh Thyr_Ag 153.6352357 2.544346e-11 6
## 12 AhHyd_Ag Thyr_Ag 380.7075634 2.344408e-24 12
## 13 AhHyd_Inh Thyr_Ag 0.0000000 1.000000e+00 0
## 14 Thyr_Ag Thyr_Inh 0.0000000 1.000000e+00 0
## 15 Thyr_Inh Thyr_Inh 1.0000000 1.000000e+00 188
## 16 Ret_Ag Thyr_Inh 10.0416079 1.296458e-45 92
## 17 Ret_Inh Thyr_Inh 13.0531334 8.534049e-02 1
## 18 Estr_Ag Thyr_Inh 1.8869453 1.246963e-02 18
## 19 Andr_Ag Thyr_Inh 0.0000000 1.000000e+00 0
## 20 Andr_Inh Thyr_Inh 0.0000000 1.000000e+00 0
## 21 GC_Ag Thyr_Inh 0.0000000 1.000000e+00 0
## 22 GC_Inh Thyr_Inh 31.9894230 3.521227e-63 65
## 23 LivX_Ag Thyr_Inh 104.3893984 1.464476e-154 123
## 24 LivX_Inh Thyr_Inh 8.3624069 1.912469e-03 4
## 25 AhHyd_Ag Thyr_Inh 0.0000000 1.000000e+00 0
## 26 AhHyd_Inh Thyr_Inh 30.9318073 1.943615e-09 8
## 27 Thyr_Ag Ret_Ag 0.9847119 6.150185e-01 2
## 28 Thyr_Inh Ret_Ag 10.0416079 1.296458e-45 92
## 29 Ret_Ag Ret_Ag 1.0000000 1.000000e+00 1369
## 30 Ret_Inh Ret_Ag 3.9422335 1.306392e-01 2
## 31 Estr_Ag Ret_Ag 13.6832853 1.370389e-215 401
## 32 Andr_Ag Ret_Ag 3.2836910 3.208514e-01 1
## 33 Andr_Inh Ret_Ag 0.0000000 1.000000e+00 0
## 34 GC_Ag Ret_Ag 0.0000000 1.000000e+00 0
## 35 GC_Inh Ret_Ag 2.5510737 3.519149e-09 61
## 36 LivX_Ag Ret_Ag 13.9349772 6.406226e-118 210
## 37 LivX_Inh Ret_Ag 1.6439679 1.863785e-01 6
## 38 AhHyd_Ag Ret_Ag 0.3507583 9.749612e-01 2
## 39 AhHyd_Inh Ret_Ag 14.1076574 4.044052e-11 17
## 40 Thyr_Ag Ret_Inh 1072.5595526 1.260372e-10 4
## 41 Thyr_Inh Ret_Inh 13.0531334 8.534049e-02 1
## 42 Ret_Ag Ret_Inh 3.9422335 1.306392e-01 2
## 43 Ret_Inh Ret_Inh 1.0000000 1.000000e+00 7
## 44 Estr_Ag Ret_Inh 13.2688496 4.580383e-03 3
## 45 Andr_Ag Ret_Inh 2628.7315517 1.142304e-06 2
## 46 Andr_Inh Ret_Inh 347.8754566 3.765714e-03 1
## 47 GC_Ag Ret_Inh 0.0000000 1.000000e+00 0
## 48 GC_Inh Ret_Inh 8.0219944 1.344023e-01 1
## 49 LivX_Ag Ret_Inh 6.3073195 1.671862e-01 1
## 50 LivX_Inh Ret_Inh 2421.3291551 2.462733e-15 6
## 51 AhHyd_Ag Ret_Inh 104.9669442 3.109100e-04 2
## 52 AhHyd_Inh Ret_Inh 0.0000000 1.000000e+00 0
## 53 Thyr_Ag Estr_Ag 10.1637020 1.083997e-05 8
## 54 Thyr_Inh Estr_Ag 1.8869453 1.246963e-02 18
## 55 Ret_Ag Estr_Ag 13.6832853 1.370389e-215 401
## 56 Ret_Inh Estr_Ag 13.2688496 4.580383e-03 3
## 57 Estr_Ag Estr_Ag 1.0000000 1.000000e+00 797
## 58 Andr_Ag Estr_Ag 17.6614783 1.605467e-02 2
## 59 Andr_Inh Estr_Ag 2.5205522 3.568766e-01 1
## 60 GC_Ag Estr_Ag 8.8236122 1.525330e-01 1
## 61 GC_Inh Estr_Ag 0.8515592 7.558552e-01 14
## 62 LivX_Ag Estr_Ag 4.3873765 3.359345e-21 72
## 63 LivX_Inh Estr_Ag 2.9530719 2.361772e-02 6
## 64 AhHyd_Ag Estr_Ag 3.2637058 3.526989e-03 9
## 65 AhHyd_Inh Estr_Ag 9.3823040 1.477041e-06 10
## 66 Thyr_Ag Andr_Ag 233.8786721 5.913366e-03 1
## 67 Thyr_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 68 Ret_Ag Andr_Ag 3.2836910 3.208514e-01 1
## 69 Ret_Inh Andr_Ag 2628.7315517 1.142304e-06 2
## 70 Estr_Ag Andr_Ag 17.6614783 1.605467e-02 2
## 71 Andr_Ag Andr_Ag 1.0000000 1.000000e+00 4
## 72 Andr_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 73 GC_Ag Andr_Ag 0.0000000 1.000000e+00 0
## 74 GC_Inh Andr_Ag 0.0000000 1.000000e+00 0
## 75 LivX_Ag Andr_Ag 12.6111237 9.925167e-02 1
## 76 LivX_Inh Andr_Ag 364.1133279 4.668738e-05 2
## 77 AhHyd_Ag Andr_Ag 86.1094022 1.553317e-02 1
## 78 AhHyd_Inh Andr_Ag 174.8291431 7.789380e-03 1
## 79 Thyr_Ag Andr_Inh 457.8089118 1.572835e-07 3
## 80 Thyr_Inh Andr_Inh 0.0000000 1.000000e+00 0
## 81 Ret_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 82 Ret_Inh Andr_Inh 347.8754566 3.765714e-03 1
## 83 Estr_Ag Andr_Inh 2.5205522 3.568766e-01 1
## 84 Andr_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 85 Andr_Inh Andr_Inh 1.0000000 1.000000e+00 8
## 86 GC_Ag Andr_Inh 0.0000000 1.000000e+00 0
## 87 GC_Inh Andr_Inh 6.8754749 1.520723e-01 1
## 88 LivX_Ag Andr_Inh 5.4058483 1.886756e-01 1
## 89 LivX_Inh Andr_Inh 224.9663006 1.166562e-06 3
## 90 AhHyd_Ag Andr_Inh 160.2681655 3.122823e-06 3
## 91 AhHyd_Inh Andr_Inh 0.0000000 1.000000e+00 0
## 92 Thyr_Ag GC_Ag 0.0000000 1.000000e+00 0
## 93 Thyr_Inh GC_Ag 0.0000000 1.000000e+00 0
## 94 Ret_Ag GC_Ag 0.0000000 1.000000e+00 0
## 95 Ret_Inh GC_Ag 0.0000000 1.000000e+00 0
## 96 Estr_Ag GC_Ag 8.8236122 1.525330e-01 1
## 97 Andr_Ag GC_Ag 0.0000000 1.000000e+00 0
## 98 Andr_Inh GC_Ag 0.0000000 1.000000e+00 0
## 99 GC_Ag GC_Ag 1.0000000 1.000000e+00 3
## 100 GC_Inh GC_Ag 0.0000000 1.000000e+00 0
## 101 LivX_Ag GC_Ag 18.9188897 7.540027e-02 1
## 102 LivX_Inh GC_Ag 0.0000000 1.000000e+00 0
## 103 AhHyd_Ag GC_Ag 0.0000000 1.000000e+00 0
## 104 AhHyd_Inh GC_Ag 0.0000000 1.000000e+00 0
## 105 Thyr_Ag GC_Inh 0.0000000 1.000000e+00 0
## 106 Thyr_Inh GC_Inh 31.9894230 3.521227e-63 65
## 107 Ret_Ag GC_Inh 2.5510737 3.519149e-09 61
## 108 Ret_Inh GC_Inh 8.0219944 1.344023e-01 1
## 109 Estr_Ag GC_Inh 0.8515592 7.558552e-01 14
## 110 Andr_Ag GC_Inh 0.0000000 1.000000e+00 0
## 111 Andr_Inh GC_Inh 6.8754749 1.520723e-01 1
## 112 GC_Ag GC_Inh 0.0000000 1.000000e+00 0
## 113 GC_Inh GC_Inh 1.0000000 1.000000e+00 303
## 114 LivX_Ag GC_Inh 13.0654542 8.311940e-45 68
## 115 LivX_Inh GC_Inh 15.4730269 8.906368e-09 10
## 116 AhHyd_Ag GC_Inh 0.8417655 6.982025e-01 1
## 117 AhHyd_Inh GC_Inh 5.5834179 2.077014e-02 3
## 118 Thyr_Ag LivX_Ag 0.0000000 1.000000e+00 0
## 119 Thyr_Inh LivX_Ag 104.3893984 1.464476e-154 123
## 120 Ret_Ag LivX_Ag 13.9349772 6.406226e-118 210
## 121 Ret_Inh LivX_Ag 6.3073195 1.671862e-01 1
## 122 Estr_Ag LivX_Ag 4.3873765 3.359345e-21 72
## 123 Andr_Ag LivX_Ag 12.6111237 9.925167e-02 1
## 124 Andr_Inh LivX_Ag 5.4058483 1.886756e-01 1
## 125 GC_Ag LivX_Ag 18.9188897 7.540027e-02 1
## 126 GC_Inh LivX_Ag 13.0654542 8.311940e-45 68
## 127 LivX_Ag LivX_Ag 1.0000000 1.000000e+00 383
## 128 LivX_Inh LivX_Ag 21.7800158 5.928677e-14 15
## 129 AhHyd_Ag LivX_Ag 0.6618125 7.809545e-01 1
## 130 AhHyd_Inh LivX_Ag 55.8396611 2.721352e-20 17
## 131 Thyr_Ag LivX_Inh 153.6352357 2.544346e-11 6
## 132 Thyr_Inh LivX_Inh 8.3624069 1.912469e-03 4
## 133 Ret_Ag LivX_Inh 1.6439679 1.863785e-01 6
## 134 Ret_Inh LivX_Inh 2421.3291551 2.462733e-15 6
## 135 Estr_Ag LivX_Inh 2.9530719 2.361772e-02 6
## 136 Andr_Ag LivX_Inh 364.1133279 4.668738e-05 2
## 137 Andr_Inh LivX_Inh 224.9663006 1.166562e-06 3
## 138 GC_Ag LivX_Inh 0.0000000 1.000000e+00 0
## 139 GC_Inh LivX_Inh 15.4730269 8.906368e-09 10
## 140 LivX_Ag LivX_Inh 21.7800158 5.928677e-14 15
## 141 LivX_Inh LivX_Inh 1.0000000 1.000000e+00 42
## 142 AhHyd_Ag LivX_Inh 20.6081686 5.825559e-04 3
## 143 AhHyd_Inh LivX_Inh 27.3380477 3.020683e-03 2
## 144 Thyr_Ag AhHyd_Ag 380.7075634 2.344408e-24 12
## 145 Thyr_Inh AhHyd_Ag 0.0000000 1.000000e+00 0
## 146 Ret_Ag AhHyd_Ag 0.3507583 9.749612e-01 2
## 147 Ret_Inh AhHyd_Ag 104.9669442 3.109100e-04 2
## 148 Estr_Ag AhHyd_Ag 3.2637058 3.526989e-03 9
## 149 Andr_Ag AhHyd_Ag 86.1094022 1.553317e-02 1
## 150 Andr_Inh AhHyd_Ag 160.2681655 3.122823e-06 3
## 151 GC_Ag AhHyd_Ag 0.0000000 1.000000e+00 0
## 152 GC_Inh AhHyd_Ag 0.8417655 6.982025e-01 1
## 153 LivX_Ag AhHyd_Ag 0.6618125 7.809545e-01 1
## 154 LivX_Inh AhHyd_Ag 20.6081686 5.825559e-04 3
## 155 AhHyd_Ag AhHyd_Ag 1.0000000 1.000000e+00 58
## 156 AhHyd_Inh AhHyd_Ag 9.2478668 1.073807e-01 1
## 157 Thyr_Ag AhHyd_Inh 0.0000000 1.000000e+00 0
## 158 Thyr_Inh AhHyd_Inh 30.9318073 1.943615e-09 8
## 159 Ret_Ag AhHyd_Inh 14.1076574 4.044052e-11 17
## 160 Ret_Inh AhHyd_Inh 0.0000000 1.000000e+00 0
## 161 Estr_Ag AhHyd_Inh 9.3823040 1.477041e-06 10
## 162 Andr_Ag AhHyd_Inh 174.8291431 7.789380e-03 1
## 163 Andr_Inh AhHyd_Inh 0.0000000 1.000000e+00 0
## 164 GC_Ag AhHyd_Inh 0.0000000 1.000000e+00 0
## 165 GC_Inh AhHyd_Inh 5.5834179 2.077014e-02 3
## 166 LivX_Ag AhHyd_Inh 55.8396611 2.721352e-20 17
## 167 LivX_Inh AhHyd_Inh 27.3380477 3.020683e-03 2
## 168 AhHyd_Ag AhHyd_Inh 9.2478668 1.073807e-01 1
## 169 AhHyd_Inh AhHyd_Inh 1.0000000 1.000000e+00 29DotPlot: visualization
I select as significant overlaps having an OR > 2 and at least 25 overlapping genes. Dots are shown for PVals < 0.01 (set in the plot). Max value in the plot must be set according to minimum PVal to avoid dots not to be shown.
cols <- viridis::cividis(100)[1:80]
ResSel <- dplyr::filter(ResMod, OR > 2) %>% dplyr::filter(Numbers > 25)
min(ResSel$Pval)## [1] 1.370389e-215max(ResSel$OR)## [1] 104.3894Dot <- ggplot(ResSel, aes(DEGs, KBase, label=Numbers)) +
geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1)) +
ggtitle('Overlap across down-regulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_DownReg.pdf'), width=8, height=8)6.3 Visualize overlap results selectively for retinoic, liverX, estrogen, thyroid
Selection
Path <- c('Thyr_Ag', 'Thyr_Inh', 'Ret_Ag', 'Ret_Inh', 'Estr_Ag', 'LivX_Ag', 'LivX_Inh')
ResPath <- ResSel[ResSel$DEGs %in% Path & ResSel$KBase %in% Path, ]
ResPath
## DEGs KBase OR Pval Numbers
## 1 Ret_Ag Thyr_Inh 10.041608 1.296458e-45 92
## 3 LivX_Ag Thyr_Inh 104.389398 1.464476e-154 123
## 4 Thyr_Inh Ret_Ag 10.041608 1.296458e-45 92
## 5 Estr_Ag Ret_Ag 13.683285 1.370389e-215 401
## 7 LivX_Ag Ret_Ag 13.934977 6.406226e-118 210
## 8 Ret_Ag Estr_Ag 13.683285 1.370389e-215 401
## 9 LivX_Ag Estr_Ag 4.387377 3.359345e-21 72
## 13 Thyr_Inh LivX_Ag 104.389398 1.464476e-154 123
## 14 Ret_Ag LivX_Ag 13.934977 6.406226e-118 210
## 15 Estr_Ag LivX_Ag 4.387377 3.359345e-21 72DotPlot: visualization
cols <- viridis::cividis(100)[1:80]
ResPath <- dplyr::filter(ResPath, OR > 2) %>% dplyr::filter(Numbers > 25)
min(ResPath$Pval)## [1] 1.370389e-215max(ResPath$OR)## [1] 104.3894Dot <- ggplot(ResPath, aes(DEGs, KBase, label=Numbers)) +
geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1))+
ggtitle('Overlap across down-regulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_DownReg_Selected.pdf'), width=8, height=8)7. Comparison across pathways: Agonist versus Inhibitor analysis
7.1 Perform Overlap
DEGs_AgvsInh <- list(
Thyr_AgvsInh_Up= row.names(DEA$Thyr$AgvsInh$DEGs[DEA$Thyr$AgvsInh$DEGs$log2FoldChange > 0, ]),
Thyr_AgvsInh_Down= row.names(DEA$Thyr$AgvsInh$DEGs[DEA$Thyr$AgvsInh$DEGs$log2FoldChange < 0, ]),
Ret_AgvsInh_Up= row.names(DEA$Ret$AgvsInh$DEGs[DEA$Ret$AgvsInh$DEGs$log2FoldChange > 0, ]),
Ret_AgvsInh_Down= row.names(DEA$Ret$AgvsInh$DEGs[DEA$Ret$AgvsInh$DEGs$log2FoldChange < 0, ]),
Estr_AgvsInh_Up= row.names(DEA$Estr$AgvsInh$DEGs[DEA$Estr$AgvsInh$DEGs$log2FoldChange > 0, ]),
Estr_AgvsInh_Down= row.names(DEA$Estr$AgvsInh$DEGs[DEA$Estr$AgvsInh$DEGs$log2FoldChange < 0, ]),
Andr_AgvsInh_Up= row.names(DEA$Andr$AgvsInh$DEGs[DEA$Andr$AgvsInh$DEGs$log2FoldChange > 0, ]),
Andr_AgvsInh_Down= row.names(DEA$Andr$AgvsInh$DEGs[DEA$Andr$AgvsInh$DEGs$log2FoldChange < 0, ]),
GC_AgvsInh_Up= row.names(DEA$GC$AgvsInh$DEGs[DEA$GC$AgvsInh$DEGs$log2FoldChange > 0, ]),
GC_AgvsInh_Down= row.names(DEA$GC$AgvsInh$DEGs[DEA$GC$AgvsInh$DEGs$log2FoldChange < 0, ]),
LivX_AgvsInh_Up= row.names(DEA$LivX$AgvsInh$DEGs[DEA$LivX$AgvsInh$DEGs$log2FoldChange > 0, ]),
LivX_AgvsInh_Down= row.names(DEA$LivX$AgvsInh$DEGs[DEA$LivX$AgvsInh$DEGs$log2FoldChange < 0, ]),
AhHyd_AgvsInh_Up= row.names(DEA$AhHyd$AgvsInh$DEGs[DEA$AhHyd$AgvsInh$DEGs$log2FoldChange > 0, ]),
AhHyd_AgvsInh_Down= row.names(DEA$AhHyd$AgvsInh$DEGs[DEA$AhHyd$AgvsInh$DEGs$log2FoldChange < 0, ])
)Universe <- row.names(DEA$Ret$Agonist$Res) %>% unique()
length(Universe)
## [1] 14850OvObj <- newGOM(DEGs_AgvsInh, DEGs_AgvsInh, genome.size=length(Universe))
#print(OvObj)getMatrix(OvObj, name='intersection')
## Thyr_AgvsInh_Up Thyr_AgvsInh_Down Ret_AgvsInh_Up
## Thyr_AgvsInh_Up 155 0 10
## Thyr_AgvsInh_Down 0 239 40
## Ret_AgvsInh_Up 10 40 1463
## Ret_AgvsInh_Down 38 3 0
## Estr_AgvsInh_Up 0 0 0
## Estr_AgvsInh_Down 0 0 0
## Andr_AgvsInh_Up 0 1 8
## Andr_AgvsInh_Down 1 0 1
## GC_AgvsInh_Up 70 0 44
## GC_AgvsInh_Down 0 36 18
## LivX_AgvsInh_Up 0 38 346
## LivX_AgvsInh_Down 35 0 0
## AhHyd_AgvsInh_Up 16 0 0
## AhHyd_AgvsInh_Down 0 14 147
## Ret_AgvsInh_Down Estr_AgvsInh_Up Estr_AgvsInh_Down
## Thyr_AgvsInh_Up 38 0 0
## Thyr_AgvsInh_Down 3 0 0
## Ret_AgvsInh_Up 0 0 0
## Ret_AgvsInh_Down 962 0 0
## Estr_AgvsInh_Up 0 0 0
## Estr_AgvsInh_Down 0 0 0
## Andr_AgvsInh_Up 0 0 0
## Andr_AgvsInh_Down 6 0 0
## GC_AgvsInh_Up 36 0 0
## GC_AgvsInh_Down 0 0 0
## LivX_AgvsInh_Up 1 0 0
## LivX_AgvsInh_Down 115 0 0
## AhHyd_AgvsInh_Up 16 0 0
## AhHyd_AgvsInh_Down 1 0 0
## Andr_AgvsInh_Up Andr_AgvsInh_Down GC_AgvsInh_Up
## Thyr_AgvsInh_Up 0 1 70
## Thyr_AgvsInh_Down 1 0 0
## Ret_AgvsInh_Up 8 1 44
## Ret_AgvsInh_Down 0 6 36
## Estr_AgvsInh_Up 0 0 0
## Estr_AgvsInh_Down 0 0 0
## Andr_AgvsInh_Up 12 0 0
## Andr_AgvsInh_Down 0 11 1
## GC_AgvsInh_Up 0 1 244
## GC_AgvsInh_Down 0 0 0
## LivX_AgvsInh_Up 5 1 14
## LivX_AgvsInh_Down 0 2 28
## AhHyd_AgvsInh_Up 0 1 15
## AhHyd_AgvsInh_Down 3 0 1
## GC_AgvsInh_Down LivX_AgvsInh_Up LivX_AgvsInh_Down
## Thyr_AgvsInh_Up 0 0 35
## Thyr_AgvsInh_Down 36 38 0
## Ret_AgvsInh_Up 18 346 0
## Ret_AgvsInh_Down 0 1 115
## Estr_AgvsInh_Up 0 0 0
## Estr_AgvsInh_Down 0 0 0
## Andr_AgvsInh_Up 0 5 0
## Andr_AgvsInh_Down 0 1 2
## GC_AgvsInh_Up 0 14 28
## GC_AgvsInh_Down 56 14 1
## LivX_AgvsInh_Up 14 440 0
## LivX_AgvsInh_Down 1 0 174
## AhHyd_AgvsInh_Up 0 1 14
## AhHyd_AgvsInh_Down 11 101 0
## AhHyd_AgvsInh_Up AhHyd_AgvsInh_Down
## Thyr_AgvsInh_Up 16 0
## Thyr_AgvsInh_Down 0 14
## Ret_AgvsInh_Up 0 147
## Ret_AgvsInh_Down 16 1
## Estr_AgvsInh_Up 0 0
## Estr_AgvsInh_Down 0 0
## Andr_AgvsInh_Up 0 3
## Andr_AgvsInh_Down 1 0
## GC_AgvsInh_Up 15 1
## GC_AgvsInh_Down 0 11
## LivX_AgvsInh_Up 1 101
## LivX_AgvsInh_Down 14 0
## AhHyd_AgvsInh_Up 43 0
## AhHyd_AgvsInh_Down 0 243getMatrix(OvObj, name='pval')
## Thyr_AgvsInh_Up Thyr_AgvsInh_Down Ret_AgvsInh_Up
## Thyr_AgvsInh_Up 0.000000e+00 1.000000e+00 9.483314e-01
## Thyr_AgvsInh_Down 1.000000e+00 0.000000e+00 5.862014e-04
## Ret_AgvsInh_Up 9.483314e-01 5.862014e-04 0.000000e+00
## Ret_AgvsInh_Down 5.098246e-13 9.999845e-01 1.000000e+00
## Estr_AgvsInh_Up 1.000000e+00 1.000000e+00 1.000000e+00
## Estr_AgvsInh_Down 1.000000e+00 1.000000e+00 1.000000e+00
## Andr_AgvsInh_Up 1.000000e+00 1.769803e-01 3.000147e-06
## Andr_AgvsInh_Down 1.090414e-01 1.000000e+00 6.805896e-01
## GC_AgvsInh_Up 1.288494e-85 1.000000e+00 5.570130e-05
## GC_AgvsInh_Down 1.000000e+00 1.074168e-51 3.792900e-06
## LivX_AgvsInh_Up 1.000000e+00 1.555239e-17 5.369891e-272
## LivX_AgvsInh_Down 1.560632e-35 1.000000e+00 1.000000e+00
## AhHyd_AgvsInh_Up 1.874095e-21 1.000000e+00 1.000000e+00
## AhHyd_AgvsInh_Down 1.000000e+00 4.016461e-05 4.985116e-86
## Ret_AgvsInh_Down Estr_AgvsInh_Up Estr_AgvsInh_Down
## Thyr_AgvsInh_Up 5.098246e-13 1 1
## Thyr_AgvsInh_Down 9.999845e-01 1 1
## Ret_AgvsInh_Up 1.000000e+00 1 1
## Ret_AgvsInh_Down 0.000000e+00 1 1
## Estr_AgvsInh_Up 1.000000e+00 1 1
## Estr_AgvsInh_Down 1.000000e+00 1 1
## Andr_AgvsInh_Up 1.000000e+00 1 1
## Andr_AgvsInh_Down 2.535003e-05 1 1
## GC_AgvsInh_Up 2.937147e-06 1 1
## GC_AgvsInh_Down 1.000000e+00 1 1
## LivX_AgvsInh_Up 1.000000e+00 1 1
## LivX_AgvsInh_Down 1.312420e-94 1 1
## AhHyd_AgvsInh_Up 4.281741e-09 1 1
## AhHyd_AgvsInh_Down 9.999999e-01 1 1
## Andr_AgvsInh_Up Andr_AgvsInh_Down GC_AgvsInh_Up
## Thyr_AgvsInh_Up 1.000000e+00 1.090414e-01 1.288494e-85
## Thyr_AgvsInh_Down 1.769803e-01 1.000000e+00 1.000000e+00
## Ret_AgvsInh_Up 3.000147e-06 6.805896e-01 5.570130e-05
## Ret_AgvsInh_Down 1.000000e+00 2.535003e-05 2.937147e-06
## Estr_AgvsInh_Up 1.000000e+00 1.000000e+00 1.000000e+00
## Estr_AgvsInh_Down 1.000000e+00 1.000000e+00 1.000000e+00
## Andr_AgvsInh_Up 4.183601e-42 1.000000e+00 1.000000e+00
## Andr_AgvsInh_Down 1.000000e+00 5.173371e-39 1.666520e-01
## GC_AgvsInh_Up 1.000000e+00 1.666520e-01 0.000000e+00
## GC_AgvsInh_Down 1.000000e+00 1.000000e+00 1.000000e+00
## LivX_AgvsInh_Up 1.488468e-05 2.817698e-01 1.419070e-02
## LivX_AgvsInh_Down 1.000000e+00 7.003976e-03 5.036623e-20
## AhHyd_AgvsInh_Up 1.000000e+00 3.140510e-02 1.123432e-16
## AhHyd_AgvsInh_Down 8.535732e-04 1.000000e+00 9.827396e-01
## GC_AgvsInh_Down LivX_AgvsInh_Up LivX_AgvsInh_Down
## Thyr_AgvsInh_Up 1.000000e+00 1.000000e+00 1.560632e-35
## Thyr_AgvsInh_Down 1.074168e-51 1.555239e-17 1.000000e+00
## Ret_AgvsInh_Up 3.792900e-06 5.369891e-272 1.000000e+00
## Ret_AgvsInh_Down 1.000000e+00 1.000000e+00 1.312420e-94
## Estr_AgvsInh_Up 1.000000e+00 1.000000e+00 1.000000e+00
## Estr_AgvsInh_Down 1.000000e+00 1.000000e+00 1.000000e+00
## Andr_AgvsInh_Up 1.000000e+00 1.488468e-05 1.000000e+00
## Andr_AgvsInh_Down 1.000000e+00 2.817698e-01 7.003976e-03
## GC_AgvsInh_Up 1.000000e+00 1.419070e-02 5.036623e-20
## GC_AgvsInh_Down 1.906696e-159 6.095751e-10 4.838040e-01
## LivX_AgvsInh_Up 6.095751e-10 0.000000e+00 1.000000e+00
## LivX_AgvsInh_Down 4.838040e-01 1.000000e+00 0.000000e+00
## AhHyd_AgvsInh_Up 1.000000e+00 7.261544e-01 3.160036e-17
## AhHyd_AgvsInh_Down 1.398295e-09 2.029891e-91 1.000000e+00
## AhHyd_AgvsInh_Up AhHyd_AgvsInh_Down
## Thyr_AgvsInh_Up 1.874095e-21 1.000000e+00
## Thyr_AgvsInh_Down 1.000000e+00 4.016461e-05
## Ret_AgvsInh_Up 1.000000e+00 4.985116e-86
## Ret_AgvsInh_Down 4.281741e-09 9.999999e-01
## Estr_AgvsInh_Up 1.000000e+00 1.000000e+00
## Estr_AgvsInh_Down 1.000000e+00 1.000000e+00
## Andr_AgvsInh_Up 1.000000e+00 8.535732e-04
## Andr_AgvsInh_Down 3.140510e-02 1.000000e+00
## GC_AgvsInh_Up 1.123432e-16 9.827396e-01
## GC_AgvsInh_Down 1.000000e+00 1.398295e-09
## LivX_AgvsInh_Up 7.261544e-01 2.029891e-91
## LivX_AgvsInh_Down 3.160036e-17 1.000000e+00
## AhHyd_AgvsInh_Up 2.650593e-127 1.000000e+00
## AhHyd_AgvsInh_Down 1.000000e+00 0.000000e+00getMatrix(OvObj, name='odds.ratio')
## Thyr_AgvsInh_Up Thyr_AgvsInh_Down Ret_AgvsInh_Up
## Thyr_AgvsInh_Up Inf 0.0000000 0.6285378
## Thyr_AgvsInh_Down 0.0000000 Inf 1.8626848
## Ret_AgvsInh_Up 0.6285378 1.8626848 Inf
## Ret_AgvsInh_Down 4.8395743 0.1809725 0.0000000
## Estr_AgvsInh_Up 0.0000000 0.0000000 0.0000000
## Estr_AgvsInh_Down 0.0000000 0.0000000 0.0000000
## Andr_AgvsInh_Up 0.0000000 5.5758129 18.3879551
## Andr_AgvsInh_Down 9.5312421 0.0000000 0.9149788
## GC_AgvsInh_Up 68.5649151 0.0000000 2.0443793
## GC_AgvsInh_Down 0.0000000 128.8985340 4.3754294
## LivX_AgvsInh_Up 0.0000000 6.6801855 43.7703727
## LivX_AgvsInh_Down 30.5073190 0.0000000 0.0000000
## AhHyd_AgvsInh_Up 62.2864885 0.0000000 0.0000000
## AhHyd_AgvsInh_Down 0.0000000 3.9071002 15.4574042
## Ret_AgvsInh_Down Estr_AgvsInh_Up Estr_AgvsInh_Down
## Thyr_AgvsInh_Up 4.83957434 0 0
## Thyr_AgvsInh_Down 0.18097249 0 0
## Ret_AgvsInh_Up 0.00000000 0 0
## Ret_AgvsInh_Down Inf 0 0
## Estr_AgvsInh_Up 0.00000000 0 0
## Estr_AgvsInh_Down 0.00000000 0 0
## Andr_AgvsInh_Up 0.00000000 0 0
## Andr_AgvsInh_Down 17.41680530 0 0
## GC_AgvsInh_Up 2.55664703 0 0
## GC_AgvsInh_Down 0.00000000 0 0
## LivX_AgvsInh_Up 0.03189191 0 0
## LivX_AgvsInh_Down 31.80114235 0 0
## AhHyd_AgvsInh_Up 8.68074512 0 0
## AhHyd_AgvsInh_Down 0.05870611 0 0
## Andr_AgvsInh_Up Andr_AgvsInh_Down GC_AgvsInh_Up
## Thyr_AgvsInh_Up 0.000000 9.5312421 68.5649151
## Thyr_AgvsInh_Down 5.575813 0.0000000 0.0000000
## Ret_AgvsInh_Up 18.387955 0.9149788 2.0443793
## Ret_AgvsInh_Down 0.000000 17.4168053 2.5566470
## Estr_AgvsInh_Up 0.000000 0.0000000 0.0000000
## Estr_AgvsInh_Down 0.000000 0.0000000 0.0000000
## Andr_AgvsInh_Up Inf 0.0000000 0.0000000
## Andr_AgvsInh_Down 0.000000 Inf 6.0046602
## GC_AgvsInh_Up 0.000000 6.0046602 Inf
## GC_AgvsInh_Down 0.000000 0.0000000 0.0000000
## LivX_AgvsInh_Up 23.628858 3.2796749 2.0259939
## LivX_AgvsInh_Down 0.000000 18.9258042 12.8353684
## AhHyd_AgvsInh_Up 0.000000 35.2077501 34.0487003
## AhHyd_AgvsInh_Down 20.267527 0.0000000 0.2442634
## GC_AgvsInh_Down LivX_AgvsInh_Up LivX_AgvsInh_Down
## Thyr_AgvsInh_Up 0.000000 0.00000000 30.507319
## Thyr_AgvsInh_Down 128.898534 6.68018550 0.000000
## Ret_AgvsInh_Up 4.375429 43.77037269 0.000000
## Ret_AgvsInh_Down 0.000000 0.03189191 31.801142
## Estr_AgvsInh_Up 0.000000 0.00000000 0.000000
## Estr_AgvsInh_Down 0.000000 0.00000000 0.000000
## Andr_AgvsInh_Up 0.000000 23.62885762 0.000000
## Andr_AgvsInh_Down 0.000000 3.27967491 18.925804
## GC_AgvsInh_Up 0.000000 2.02599393 12.835368
## GC_AgvsInh_Down Inf 11.23510761 1.536539
## LivX_AgvsInh_Up 11.235108 Inf 0.000000
## LivX_AgvsInh_Down 1.536539 0.00000000 Inf
## AhHyd_AgvsInh_Up 0.000000 0.77927094 44.052621
## AhHyd_AgvsInh_Down 15.334561 29.90344064 0.000000
## AhHyd_AgvsInh_Up AhHyd_AgvsInh_Down
## Thyr_AgvsInh_Up 62.2864885 0.00000000
## Thyr_AgvsInh_Down 0.0000000 3.90710024
## Ret_AgvsInh_Up 0.0000000 15.45740424
## Ret_AgvsInh_Down 8.6807451 0.05870611
## Estr_AgvsInh_Up 0.0000000 0.00000000
## Estr_AgvsInh_Down 0.0000000 0.00000000
## Andr_AgvsInh_Up 0.0000000 20.26752689
## Andr_AgvsInh_Down 35.2077501 0.00000000
## GC_AgvsInh_Up 34.0487003 0.24426338
## GC_AgvsInh_Down 0.0000000 15.33456104
## LivX_AgvsInh_Up 0.7792709 29.90344064
## LivX_AgvsInh_Down 44.0526213 0.00000000
## AhHyd_AgvsInh_Up Inf 0.00000000
## AhHyd_AgvsInh_Down 0.0000000 Inf7.2 Visualize overlap results
DotPlot: data preparation
OR <- data.frame(getMatrix(OvObj, name='odds.ratio'))
OR$DEGs <- row.names(OR)
OR <- gather(OR, 'KBase', 'OR', -DEGs)
PVAL <- data.frame(getMatrix(OvObj, name='pval'))
PVAL$DEGs <- row.names(PVAL)
PVAL <- gather(PVAL, 'KBase', 'PVal', -DEGs)
NUM <- data.frame(getMatrix(OvObj, name='intersection'))
NUM$DEGs <- row.names(NUM)
NUM <- gather(NUM, 'KBase', 'Numbers', -DEGs)
if(! identical(OR$DEGs, PVAL$DEGs)){
stop('Inconsistecy')
}
if(! identical(OR$DEGs, NUM$DEGs)){
stop('Inconsistecy')
}
if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}
if(! identical(OR$KBase, NUM$KBase)){
stop('Inconsistecy')
}
Res <- mutate(OR, Pval=PVAL$PVal) %>% mutate(Numbers=NUM$Numbers)
Res
## DEGs KBase OR Pval Numbers
## 1 Thyr_AgvsInh_Up Thyr_AgvsInh_Up Inf 0.000000e+00 155
## 2 Thyr_AgvsInh_Down Thyr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 3 Ret_AgvsInh_Up Thyr_AgvsInh_Up 0.62853784 9.483314e-01 10
## 4 Ret_AgvsInh_Down Thyr_AgvsInh_Up 4.83957434 5.098246e-13 38
## 5 Estr_AgvsInh_Up Thyr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 6 Estr_AgvsInh_Down Thyr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 7 Andr_AgvsInh_Up Thyr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 8 Andr_AgvsInh_Down Thyr_AgvsInh_Up 9.53124213 1.090414e-01 1
## 9 GC_AgvsInh_Up Thyr_AgvsInh_Up 68.56491514 1.288494e-85 70
## 10 GC_AgvsInh_Down Thyr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 11 LivX_AgvsInh_Up Thyr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 12 LivX_AgvsInh_Down Thyr_AgvsInh_Up 30.50731902 1.560632e-35 35
## 13 AhHyd_AgvsInh_Up Thyr_AgvsInh_Up 62.28648850 1.874095e-21 16
## 14 AhHyd_AgvsInh_Down Thyr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 15 Thyr_AgvsInh_Up Thyr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 16 Thyr_AgvsInh_Down Thyr_AgvsInh_Down Inf 0.000000e+00 239
## 17 Ret_AgvsInh_Up Thyr_AgvsInh_Down 1.86268484 5.862014e-04 40
## 18 Ret_AgvsInh_Down Thyr_AgvsInh_Down 0.18097249 9.999845e-01 3
## 19 Estr_AgvsInh_Up Thyr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 20 Estr_AgvsInh_Down Thyr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 21 Andr_AgvsInh_Up Thyr_AgvsInh_Down 5.57581291 1.769803e-01 1
## 22 Andr_AgvsInh_Down Thyr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 23 GC_AgvsInh_Up Thyr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 24 GC_AgvsInh_Down Thyr_AgvsInh_Down 128.89853403 1.074168e-51 36
## 25 LivX_AgvsInh_Up Thyr_AgvsInh_Down 6.68018550 1.555239e-17 38
## 26 LivX_AgvsInh_Down Thyr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 27 AhHyd_AgvsInh_Up Thyr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 28 AhHyd_AgvsInh_Down Thyr_AgvsInh_Down 3.90710024 4.016461e-05 14
## 29 Thyr_AgvsInh_Up Ret_AgvsInh_Up 0.62853784 9.483314e-01 10
## 30 Thyr_AgvsInh_Down Ret_AgvsInh_Up 1.86268484 5.862014e-04 40
## 31 Ret_AgvsInh_Up Ret_AgvsInh_Up Inf 0.000000e+00 1463
## 32 Ret_AgvsInh_Down Ret_AgvsInh_Up 0.00000000 1.000000e+00 0
## 33 Estr_AgvsInh_Up Ret_AgvsInh_Up 0.00000000 1.000000e+00 0
## 34 Estr_AgvsInh_Down Ret_AgvsInh_Up 0.00000000 1.000000e+00 0
## 35 Andr_AgvsInh_Up Ret_AgvsInh_Up 18.38795511 3.000147e-06 8
## 36 Andr_AgvsInh_Down Ret_AgvsInh_Up 0.91497876 6.805896e-01 1
## 37 GC_AgvsInh_Up Ret_AgvsInh_Up 2.04437933 5.570130e-05 44
## 38 GC_AgvsInh_Down Ret_AgvsInh_Up 4.37542936 3.792900e-06 18
## 39 LivX_AgvsInh_Up Ret_AgvsInh_Up 43.77037269 5.369891e-272 346
## 40 LivX_AgvsInh_Down Ret_AgvsInh_Up 0.00000000 1.000000e+00 0
## 41 AhHyd_AgvsInh_Up Ret_AgvsInh_Up 0.00000000 1.000000e+00 0
## 42 AhHyd_AgvsInh_Down Ret_AgvsInh_Up 15.45740424 4.985116e-86 147
## 43 Thyr_AgvsInh_Up Ret_AgvsInh_Down 4.83957434 5.098246e-13 38
## 44 Thyr_AgvsInh_Down Ret_AgvsInh_Down 0.18097249 9.999845e-01 3
## 45 Ret_AgvsInh_Up Ret_AgvsInh_Down 0.00000000 1.000000e+00 0
## 46 Ret_AgvsInh_Down Ret_AgvsInh_Down Inf 0.000000e+00 962
## 47 Estr_AgvsInh_Up Ret_AgvsInh_Down 0.00000000 1.000000e+00 0
## 48 Estr_AgvsInh_Down Ret_AgvsInh_Down 0.00000000 1.000000e+00 0
## 49 Andr_AgvsInh_Up Ret_AgvsInh_Down 0.00000000 1.000000e+00 0
## 50 Andr_AgvsInh_Down Ret_AgvsInh_Down 17.41680530 2.535003e-05 6
## 51 GC_AgvsInh_Up Ret_AgvsInh_Down 2.55664703 2.937147e-06 36
## 52 GC_AgvsInh_Down Ret_AgvsInh_Down 0.00000000 1.000000e+00 0
## 53 LivX_AgvsInh_Up Ret_AgvsInh_Down 0.03189191 1.000000e+00 1
## 54 LivX_AgvsInh_Down Ret_AgvsInh_Down 31.80114235 1.312420e-94 115
## 55 AhHyd_AgvsInh_Up Ret_AgvsInh_Down 8.68074512 4.281741e-09 16
## 56 AhHyd_AgvsInh_Down Ret_AgvsInh_Down 0.05870611 9.999999e-01 1
## 57 Thyr_AgvsInh_Up Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 58 Thyr_AgvsInh_Down Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 59 Ret_AgvsInh_Up Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 60 Ret_AgvsInh_Down Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 61 Estr_AgvsInh_Up Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 62 Estr_AgvsInh_Down Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 63 Andr_AgvsInh_Up Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 64 Andr_AgvsInh_Down Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 65 GC_AgvsInh_Up Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 66 GC_AgvsInh_Down Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 67 LivX_AgvsInh_Up Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 68 LivX_AgvsInh_Down Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 69 AhHyd_AgvsInh_Up Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 70 AhHyd_AgvsInh_Down Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 71 Thyr_AgvsInh_Up Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 72 Thyr_AgvsInh_Down Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 73 Ret_AgvsInh_Up Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 74 Ret_AgvsInh_Down Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 75 Estr_AgvsInh_Up Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 76 Estr_AgvsInh_Down Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 77 Andr_AgvsInh_Up Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 78 Andr_AgvsInh_Down Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 79 GC_AgvsInh_Up Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 80 GC_AgvsInh_Down Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 81 LivX_AgvsInh_Up Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 82 LivX_AgvsInh_Down Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 83 AhHyd_AgvsInh_Up Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 84 AhHyd_AgvsInh_Down Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 85 Thyr_AgvsInh_Up Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 86 Thyr_AgvsInh_Down Andr_AgvsInh_Up 5.57581291 1.769803e-01 1
## 87 Ret_AgvsInh_Up Andr_AgvsInh_Up 18.38795511 3.000147e-06 8
## 88 Ret_AgvsInh_Down Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 89 Estr_AgvsInh_Up Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 90 Estr_AgvsInh_Down Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 91 Andr_AgvsInh_Up Andr_AgvsInh_Up Inf 4.183601e-42 12
## 92 Andr_AgvsInh_Down Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 93 GC_AgvsInh_Up Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 94 GC_AgvsInh_Down Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 95 LivX_AgvsInh_Up Andr_AgvsInh_Up 23.62885762 1.488468e-05 5
## 96 LivX_AgvsInh_Down Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 97 AhHyd_AgvsInh_Up Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 98 AhHyd_AgvsInh_Down Andr_AgvsInh_Up 20.26752689 8.535732e-04 3
## 99 Thyr_AgvsInh_Up Andr_AgvsInh_Down 9.53124213 1.090414e-01 1
## 100 Thyr_AgvsInh_Down Andr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 101 Ret_AgvsInh_Up Andr_AgvsInh_Down 0.91497876 6.805896e-01 1
## 102 Ret_AgvsInh_Down Andr_AgvsInh_Down 17.41680530 2.535003e-05 6
## 103 Estr_AgvsInh_Up Andr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 104 Estr_AgvsInh_Down Andr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 105 Andr_AgvsInh_Up Andr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 106 Andr_AgvsInh_Down Andr_AgvsInh_Down Inf 5.173371e-39 11
## 107 GC_AgvsInh_Up Andr_AgvsInh_Down 6.00466024 1.666520e-01 1
## 108 GC_AgvsInh_Down Andr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 109 LivX_AgvsInh_Up Andr_AgvsInh_Down 3.27967491 2.817698e-01 1
## 110 LivX_AgvsInh_Down Andr_AgvsInh_Down 18.92580425 7.003976e-03 2
## 111 AhHyd_AgvsInh_Up Andr_AgvsInh_Down 35.20775010 3.140510e-02 1
## 112 AhHyd_AgvsInh_Down Andr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 113 Thyr_AgvsInh_Up GC_AgvsInh_Up 68.56491514 1.288494e-85 70
## 114 Thyr_AgvsInh_Down GC_AgvsInh_Up 0.00000000 1.000000e+00 0
## 115 Ret_AgvsInh_Up GC_AgvsInh_Up 2.04437933 5.570130e-05 44
## 116 Ret_AgvsInh_Down GC_AgvsInh_Up 2.55664703 2.937147e-06 36
## 117 Estr_AgvsInh_Up GC_AgvsInh_Up 0.00000000 1.000000e+00 0
## 118 Estr_AgvsInh_Down GC_AgvsInh_Up 0.00000000 1.000000e+00 0
## 119 Andr_AgvsInh_Up GC_AgvsInh_Up 0.00000000 1.000000e+00 0
## 120 Andr_AgvsInh_Down GC_AgvsInh_Up 6.00466024 1.666520e-01 1
## 121 GC_AgvsInh_Up GC_AgvsInh_Up Inf 0.000000e+00 244
## 122 GC_AgvsInh_Down GC_AgvsInh_Up 0.00000000 1.000000e+00 0
## 123 LivX_AgvsInh_Up GC_AgvsInh_Up 2.02599393 1.419070e-02 14
## 124 LivX_AgvsInh_Down GC_AgvsInh_Up 12.83536838 5.036623e-20 28
## 125 AhHyd_AgvsInh_Up GC_AgvsInh_Up 34.04870032 1.123432e-16 15
## 126 AhHyd_AgvsInh_Down GC_AgvsInh_Up 0.24426338 9.827396e-01 1
## 127 Thyr_AgvsInh_Up GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 128 Thyr_AgvsInh_Down GC_AgvsInh_Down 128.89853403 1.074168e-51 36
## 129 Ret_AgvsInh_Up GC_AgvsInh_Down 4.37542936 3.792900e-06 18
## 130 Ret_AgvsInh_Down GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 131 Estr_AgvsInh_Up GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 132 Estr_AgvsInh_Down GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 133 Andr_AgvsInh_Up GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 134 Andr_AgvsInh_Down GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 135 GC_AgvsInh_Up GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 136 GC_AgvsInh_Down GC_AgvsInh_Down Inf 1.906696e-159 56
## 137 LivX_AgvsInh_Up GC_AgvsInh_Down 11.23510761 6.095751e-10 14
## 138 LivX_AgvsInh_Down GC_AgvsInh_Down 1.53653872 4.838040e-01 1
## 139 AhHyd_AgvsInh_Up GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 140 AhHyd_AgvsInh_Down GC_AgvsInh_Down 15.33456104 1.398295e-09 11
## 141 Thyr_AgvsInh_Up LivX_AgvsInh_Up 0.00000000 1.000000e+00 0
## 142 Thyr_AgvsInh_Down LivX_AgvsInh_Up 6.68018550 1.555239e-17 38
## 143 Ret_AgvsInh_Up LivX_AgvsInh_Up 43.77037269 5.369891e-272 346
## 144 Ret_AgvsInh_Down LivX_AgvsInh_Up 0.03189191 1.000000e+00 1
## 145 Estr_AgvsInh_Up LivX_AgvsInh_Up 0.00000000 1.000000e+00 0
## 146 Estr_AgvsInh_Down LivX_AgvsInh_Up 0.00000000 1.000000e+00 0
## 147 Andr_AgvsInh_Up LivX_AgvsInh_Up 23.62885762 1.488468e-05 5
## 148 Andr_AgvsInh_Down LivX_AgvsInh_Up 3.27967491 2.817698e-01 1
## 149 GC_AgvsInh_Up LivX_AgvsInh_Up 2.02599393 1.419070e-02 14
## 150 GC_AgvsInh_Down LivX_AgvsInh_Up 11.23510761 6.095751e-10 14
## 151 LivX_AgvsInh_Up LivX_AgvsInh_Up Inf 0.000000e+00 440
## 152 LivX_AgvsInh_Down LivX_AgvsInh_Up 0.00000000 1.000000e+00 0
## 153 AhHyd_AgvsInh_Up LivX_AgvsInh_Up 0.77927094 7.261544e-01 1
## 154 AhHyd_AgvsInh_Down LivX_AgvsInh_Up 29.90344064 2.029891e-91 101
## 155 Thyr_AgvsInh_Up LivX_AgvsInh_Down 30.50731902 1.560632e-35 35
## 156 Thyr_AgvsInh_Down LivX_AgvsInh_Down 0.00000000 1.000000e+00 0
## 157 Ret_AgvsInh_Up LivX_AgvsInh_Down 0.00000000 1.000000e+00 0
## 158 Ret_AgvsInh_Down LivX_AgvsInh_Down 31.80114235 1.312420e-94 115
## 159 Estr_AgvsInh_Up LivX_AgvsInh_Down 0.00000000 1.000000e+00 0
## 160 Estr_AgvsInh_Down LivX_AgvsInh_Down 0.00000000 1.000000e+00 0
## 161 Andr_AgvsInh_Up LivX_AgvsInh_Down 0.00000000 1.000000e+00 0
## 162 Andr_AgvsInh_Down LivX_AgvsInh_Down 18.92580425 7.003976e-03 2
## 163 GC_AgvsInh_Up LivX_AgvsInh_Down 12.83536838 5.036623e-20 28
## 164 GC_AgvsInh_Down LivX_AgvsInh_Down 1.53653872 4.838040e-01 1
## 165 LivX_AgvsInh_Up LivX_AgvsInh_Down 0.00000000 1.000000e+00 0
## 166 LivX_AgvsInh_Down LivX_AgvsInh_Down Inf 0.000000e+00 174
## 167 AhHyd_AgvsInh_Up LivX_AgvsInh_Down 44.05262135 3.160036e-17 14
## 168 AhHyd_AgvsInh_Down LivX_AgvsInh_Down 0.00000000 1.000000e+00 0
## 169 Thyr_AgvsInh_Up AhHyd_AgvsInh_Up 62.28648850 1.874095e-21 16
## 170 Thyr_AgvsInh_Down AhHyd_AgvsInh_Up 0.00000000 1.000000e+00 0
## 171 Ret_AgvsInh_Up AhHyd_AgvsInh_Up 0.00000000 1.000000e+00 0
## 172 Ret_AgvsInh_Down AhHyd_AgvsInh_Up 8.68074512 4.281741e-09 16
## 173 Estr_AgvsInh_Up AhHyd_AgvsInh_Up 0.00000000 1.000000e+00 0
## 174 Estr_AgvsInh_Down AhHyd_AgvsInh_Up 0.00000000 1.000000e+00 0
## 175 Andr_AgvsInh_Up AhHyd_AgvsInh_Up 0.00000000 1.000000e+00 0
## 176 Andr_AgvsInh_Down AhHyd_AgvsInh_Up 35.20775010 3.140510e-02 1
## 177 GC_AgvsInh_Up AhHyd_AgvsInh_Up 34.04870032 1.123432e-16 15
## 178 GC_AgvsInh_Down AhHyd_AgvsInh_Up 0.00000000 1.000000e+00 0
## 179 LivX_AgvsInh_Up AhHyd_AgvsInh_Up 0.77927094 7.261544e-01 1
## 180 LivX_AgvsInh_Down AhHyd_AgvsInh_Up 44.05262135 3.160036e-17 14
## 181 AhHyd_AgvsInh_Up AhHyd_AgvsInh_Up Inf 2.650593e-127 43
## 182 AhHyd_AgvsInh_Down AhHyd_AgvsInh_Up 0.00000000 1.000000e+00 0
## 183 Thyr_AgvsInh_Up AhHyd_AgvsInh_Down 0.00000000 1.000000e+00 0
## 184 Thyr_AgvsInh_Down AhHyd_AgvsInh_Down 3.90710024 4.016461e-05 14
## 185 Ret_AgvsInh_Up AhHyd_AgvsInh_Down 15.45740424 4.985116e-86 147
## 186 Ret_AgvsInh_Down AhHyd_AgvsInh_Down 0.05870611 9.999999e-01 1
## 187 Estr_AgvsInh_Up AhHyd_AgvsInh_Down 0.00000000 1.000000e+00 0
## 188 Estr_AgvsInh_Down AhHyd_AgvsInh_Down 0.00000000 1.000000e+00 0
## 189 Andr_AgvsInh_Up AhHyd_AgvsInh_Down 20.26752689 8.535732e-04 3
## 190 Andr_AgvsInh_Down AhHyd_AgvsInh_Down 0.00000000 1.000000e+00 0
## 191 GC_AgvsInh_Up AhHyd_AgvsInh_Down 0.24426338 9.827396e-01 1
## 192 GC_AgvsInh_Down AhHyd_AgvsInh_Down 15.33456104 1.398295e-09 11
## 193 LivX_AgvsInh_Up AhHyd_AgvsInh_Down 29.90344064 2.029891e-91 101
## 194 LivX_AgvsInh_Down AhHyd_AgvsInh_Down 0.00000000 1.000000e+00 0
## 195 AhHyd_AgvsInh_Up AhHyd_AgvsInh_Down 0.00000000 1.000000e+00 0
## 196 AhHyd_AgvsInh_Down AhHyd_AgvsInh_Down Inf 0.000000e+00 243ResMod <- Res
ResMod[ResMod$DEGs == ResMod$KBase, ]$OR <- 1
ResMod[ResMod$DEGs == ResMod$KBase, ]$Pval <- 1
ResMod
## DEGs KBase OR Pval Numbers
## 1 Thyr_AgvsInh_Up Thyr_AgvsInh_Up 1.00000000 1.000000e+00 155
## 2 Thyr_AgvsInh_Down Thyr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 3 Ret_AgvsInh_Up Thyr_AgvsInh_Up 0.62853784 9.483314e-01 10
## 4 Ret_AgvsInh_Down Thyr_AgvsInh_Up 4.83957434 5.098246e-13 38
## 5 Estr_AgvsInh_Up Thyr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 6 Estr_AgvsInh_Down Thyr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 7 Andr_AgvsInh_Up Thyr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 8 Andr_AgvsInh_Down Thyr_AgvsInh_Up 9.53124213 1.090414e-01 1
## 9 GC_AgvsInh_Up Thyr_AgvsInh_Up 68.56491514 1.288494e-85 70
## 10 GC_AgvsInh_Down Thyr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 11 LivX_AgvsInh_Up Thyr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 12 LivX_AgvsInh_Down Thyr_AgvsInh_Up 30.50731902 1.560632e-35 35
## 13 AhHyd_AgvsInh_Up Thyr_AgvsInh_Up 62.28648850 1.874095e-21 16
## 14 AhHyd_AgvsInh_Down Thyr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 15 Thyr_AgvsInh_Up Thyr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 16 Thyr_AgvsInh_Down Thyr_AgvsInh_Down 1.00000000 1.000000e+00 239
## 17 Ret_AgvsInh_Up Thyr_AgvsInh_Down 1.86268484 5.862014e-04 40
## 18 Ret_AgvsInh_Down Thyr_AgvsInh_Down 0.18097249 9.999845e-01 3
## 19 Estr_AgvsInh_Up Thyr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 20 Estr_AgvsInh_Down Thyr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 21 Andr_AgvsInh_Up Thyr_AgvsInh_Down 5.57581291 1.769803e-01 1
## 22 Andr_AgvsInh_Down Thyr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 23 GC_AgvsInh_Up Thyr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 24 GC_AgvsInh_Down Thyr_AgvsInh_Down 128.89853403 1.074168e-51 36
## 25 LivX_AgvsInh_Up Thyr_AgvsInh_Down 6.68018550 1.555239e-17 38
## 26 LivX_AgvsInh_Down Thyr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 27 AhHyd_AgvsInh_Up Thyr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 28 AhHyd_AgvsInh_Down Thyr_AgvsInh_Down 3.90710024 4.016461e-05 14
## 29 Thyr_AgvsInh_Up Ret_AgvsInh_Up 0.62853784 9.483314e-01 10
## 30 Thyr_AgvsInh_Down Ret_AgvsInh_Up 1.86268484 5.862014e-04 40
## 31 Ret_AgvsInh_Up Ret_AgvsInh_Up 1.00000000 1.000000e+00 1463
## 32 Ret_AgvsInh_Down Ret_AgvsInh_Up 0.00000000 1.000000e+00 0
## 33 Estr_AgvsInh_Up Ret_AgvsInh_Up 0.00000000 1.000000e+00 0
## 34 Estr_AgvsInh_Down Ret_AgvsInh_Up 0.00000000 1.000000e+00 0
## 35 Andr_AgvsInh_Up Ret_AgvsInh_Up 18.38795511 3.000147e-06 8
## 36 Andr_AgvsInh_Down Ret_AgvsInh_Up 0.91497876 6.805896e-01 1
## 37 GC_AgvsInh_Up Ret_AgvsInh_Up 2.04437933 5.570130e-05 44
## 38 GC_AgvsInh_Down Ret_AgvsInh_Up 4.37542936 3.792900e-06 18
## 39 LivX_AgvsInh_Up Ret_AgvsInh_Up 43.77037269 5.369891e-272 346
## 40 LivX_AgvsInh_Down Ret_AgvsInh_Up 0.00000000 1.000000e+00 0
## 41 AhHyd_AgvsInh_Up Ret_AgvsInh_Up 0.00000000 1.000000e+00 0
## 42 AhHyd_AgvsInh_Down Ret_AgvsInh_Up 15.45740424 4.985116e-86 147
## 43 Thyr_AgvsInh_Up Ret_AgvsInh_Down 4.83957434 5.098246e-13 38
## 44 Thyr_AgvsInh_Down Ret_AgvsInh_Down 0.18097249 9.999845e-01 3
## 45 Ret_AgvsInh_Up Ret_AgvsInh_Down 0.00000000 1.000000e+00 0
## 46 Ret_AgvsInh_Down Ret_AgvsInh_Down 1.00000000 1.000000e+00 962
## 47 Estr_AgvsInh_Up Ret_AgvsInh_Down 0.00000000 1.000000e+00 0
## 48 Estr_AgvsInh_Down Ret_AgvsInh_Down 0.00000000 1.000000e+00 0
## 49 Andr_AgvsInh_Up Ret_AgvsInh_Down 0.00000000 1.000000e+00 0
## 50 Andr_AgvsInh_Down Ret_AgvsInh_Down 17.41680530 2.535003e-05 6
## 51 GC_AgvsInh_Up Ret_AgvsInh_Down 2.55664703 2.937147e-06 36
## 52 GC_AgvsInh_Down Ret_AgvsInh_Down 0.00000000 1.000000e+00 0
## 53 LivX_AgvsInh_Up Ret_AgvsInh_Down 0.03189191 1.000000e+00 1
## 54 LivX_AgvsInh_Down Ret_AgvsInh_Down 31.80114235 1.312420e-94 115
## 55 AhHyd_AgvsInh_Up Ret_AgvsInh_Down 8.68074512 4.281741e-09 16
## 56 AhHyd_AgvsInh_Down Ret_AgvsInh_Down 0.05870611 9.999999e-01 1
## 57 Thyr_AgvsInh_Up Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 58 Thyr_AgvsInh_Down Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 59 Ret_AgvsInh_Up Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 60 Ret_AgvsInh_Down Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 61 Estr_AgvsInh_Up Estr_AgvsInh_Up 1.00000000 1.000000e+00 0
## 62 Estr_AgvsInh_Down Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 63 Andr_AgvsInh_Up Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 64 Andr_AgvsInh_Down Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 65 GC_AgvsInh_Up Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 66 GC_AgvsInh_Down Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 67 LivX_AgvsInh_Up Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 68 LivX_AgvsInh_Down Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 69 AhHyd_AgvsInh_Up Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 70 AhHyd_AgvsInh_Down Estr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 71 Thyr_AgvsInh_Up Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 72 Thyr_AgvsInh_Down Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 73 Ret_AgvsInh_Up Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 74 Ret_AgvsInh_Down Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 75 Estr_AgvsInh_Up Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 76 Estr_AgvsInh_Down Estr_AgvsInh_Down 1.00000000 1.000000e+00 0
## 77 Andr_AgvsInh_Up Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 78 Andr_AgvsInh_Down Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 79 GC_AgvsInh_Up Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 80 GC_AgvsInh_Down Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 81 LivX_AgvsInh_Up Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 82 LivX_AgvsInh_Down Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 83 AhHyd_AgvsInh_Up Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 84 AhHyd_AgvsInh_Down Estr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 85 Thyr_AgvsInh_Up Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 86 Thyr_AgvsInh_Down Andr_AgvsInh_Up 5.57581291 1.769803e-01 1
## 87 Ret_AgvsInh_Up Andr_AgvsInh_Up 18.38795511 3.000147e-06 8
## 88 Ret_AgvsInh_Down Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 89 Estr_AgvsInh_Up Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 90 Estr_AgvsInh_Down Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 91 Andr_AgvsInh_Up Andr_AgvsInh_Up 1.00000000 1.000000e+00 12
## 92 Andr_AgvsInh_Down Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 93 GC_AgvsInh_Up Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 94 GC_AgvsInh_Down Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 95 LivX_AgvsInh_Up Andr_AgvsInh_Up 23.62885762 1.488468e-05 5
## 96 LivX_AgvsInh_Down Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 97 AhHyd_AgvsInh_Up Andr_AgvsInh_Up 0.00000000 1.000000e+00 0
## 98 AhHyd_AgvsInh_Down Andr_AgvsInh_Up 20.26752689 8.535732e-04 3
## 99 Thyr_AgvsInh_Up Andr_AgvsInh_Down 9.53124213 1.090414e-01 1
## 100 Thyr_AgvsInh_Down Andr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 101 Ret_AgvsInh_Up Andr_AgvsInh_Down 0.91497876 6.805896e-01 1
## 102 Ret_AgvsInh_Down Andr_AgvsInh_Down 17.41680530 2.535003e-05 6
## 103 Estr_AgvsInh_Up Andr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 104 Estr_AgvsInh_Down Andr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 105 Andr_AgvsInh_Up Andr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 106 Andr_AgvsInh_Down Andr_AgvsInh_Down 1.00000000 1.000000e+00 11
## 107 GC_AgvsInh_Up Andr_AgvsInh_Down 6.00466024 1.666520e-01 1
## 108 GC_AgvsInh_Down Andr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 109 LivX_AgvsInh_Up Andr_AgvsInh_Down 3.27967491 2.817698e-01 1
## 110 LivX_AgvsInh_Down Andr_AgvsInh_Down 18.92580425 7.003976e-03 2
## 111 AhHyd_AgvsInh_Up Andr_AgvsInh_Down 35.20775010 3.140510e-02 1
## 112 AhHyd_AgvsInh_Down Andr_AgvsInh_Down 0.00000000 1.000000e+00 0
## 113 Thyr_AgvsInh_Up GC_AgvsInh_Up 68.56491514 1.288494e-85 70
## 114 Thyr_AgvsInh_Down GC_AgvsInh_Up 0.00000000 1.000000e+00 0
## 115 Ret_AgvsInh_Up GC_AgvsInh_Up 2.04437933 5.570130e-05 44
## 116 Ret_AgvsInh_Down GC_AgvsInh_Up 2.55664703 2.937147e-06 36
## 117 Estr_AgvsInh_Up GC_AgvsInh_Up 0.00000000 1.000000e+00 0
## 118 Estr_AgvsInh_Down GC_AgvsInh_Up 0.00000000 1.000000e+00 0
## 119 Andr_AgvsInh_Up GC_AgvsInh_Up 0.00000000 1.000000e+00 0
## 120 Andr_AgvsInh_Down GC_AgvsInh_Up 6.00466024 1.666520e-01 1
## 121 GC_AgvsInh_Up GC_AgvsInh_Up 1.00000000 1.000000e+00 244
## 122 GC_AgvsInh_Down GC_AgvsInh_Up 0.00000000 1.000000e+00 0
## 123 LivX_AgvsInh_Up GC_AgvsInh_Up 2.02599393 1.419070e-02 14
## 124 LivX_AgvsInh_Down GC_AgvsInh_Up 12.83536838 5.036623e-20 28
## 125 AhHyd_AgvsInh_Up GC_AgvsInh_Up 34.04870032 1.123432e-16 15
## 126 AhHyd_AgvsInh_Down GC_AgvsInh_Up 0.24426338 9.827396e-01 1
## 127 Thyr_AgvsInh_Up GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 128 Thyr_AgvsInh_Down GC_AgvsInh_Down 128.89853403 1.074168e-51 36
## 129 Ret_AgvsInh_Up GC_AgvsInh_Down 4.37542936 3.792900e-06 18
## 130 Ret_AgvsInh_Down GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 131 Estr_AgvsInh_Up GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 132 Estr_AgvsInh_Down GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 133 Andr_AgvsInh_Up GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 134 Andr_AgvsInh_Down GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 135 GC_AgvsInh_Up GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 136 GC_AgvsInh_Down GC_AgvsInh_Down 1.00000000 1.000000e+00 56
## 137 LivX_AgvsInh_Up GC_AgvsInh_Down 11.23510761 6.095751e-10 14
## 138 LivX_AgvsInh_Down GC_AgvsInh_Down 1.53653872 4.838040e-01 1
## 139 AhHyd_AgvsInh_Up GC_AgvsInh_Down 0.00000000 1.000000e+00 0
## 140 AhHyd_AgvsInh_Down GC_AgvsInh_Down 15.33456104 1.398295e-09 11
## 141 Thyr_AgvsInh_Up LivX_AgvsInh_Up 0.00000000 1.000000e+00 0
## 142 Thyr_AgvsInh_Down LivX_AgvsInh_Up 6.68018550 1.555239e-17 38
## 143 Ret_AgvsInh_Up LivX_AgvsInh_Up 43.77037269 5.369891e-272 346
## 144 Ret_AgvsInh_Down LivX_AgvsInh_Up 0.03189191 1.000000e+00 1
## 145 Estr_AgvsInh_Up LivX_AgvsInh_Up 0.00000000 1.000000e+00 0
## 146 Estr_AgvsInh_Down LivX_AgvsInh_Up 0.00000000 1.000000e+00 0
## 147 Andr_AgvsInh_Up LivX_AgvsInh_Up 23.62885762 1.488468e-05 5
## 148 Andr_AgvsInh_Down LivX_AgvsInh_Up 3.27967491 2.817698e-01 1
## 149 GC_AgvsInh_Up LivX_AgvsInh_Up 2.02599393 1.419070e-02 14
## 150 GC_AgvsInh_Down LivX_AgvsInh_Up 11.23510761 6.095751e-10 14
## 151 LivX_AgvsInh_Up LivX_AgvsInh_Up 1.00000000 1.000000e+00 440
## 152 LivX_AgvsInh_Down LivX_AgvsInh_Up 0.00000000 1.000000e+00 0
## 153 AhHyd_AgvsInh_Up LivX_AgvsInh_Up 0.77927094 7.261544e-01 1
## 154 AhHyd_AgvsInh_Down LivX_AgvsInh_Up 29.90344064 2.029891e-91 101
## 155 Thyr_AgvsInh_Up LivX_AgvsInh_Down 30.50731902 1.560632e-35 35
## 156 Thyr_AgvsInh_Down LivX_AgvsInh_Down 0.00000000 1.000000e+00 0
## 157 Ret_AgvsInh_Up LivX_AgvsInh_Down 0.00000000 1.000000e+00 0
## 158 Ret_AgvsInh_Down LivX_AgvsInh_Down 31.80114235 1.312420e-94 115
## 159 Estr_AgvsInh_Up LivX_AgvsInh_Down 0.00000000 1.000000e+00 0
## 160 Estr_AgvsInh_Down LivX_AgvsInh_Down 0.00000000 1.000000e+00 0
## 161 Andr_AgvsInh_Up LivX_AgvsInh_Down 0.00000000 1.000000e+00 0
## 162 Andr_AgvsInh_Down LivX_AgvsInh_Down 18.92580425 7.003976e-03 2
## 163 GC_AgvsInh_Up LivX_AgvsInh_Down 12.83536838 5.036623e-20 28
## 164 GC_AgvsInh_Down LivX_AgvsInh_Down 1.53653872 4.838040e-01 1
## 165 LivX_AgvsInh_Up LivX_AgvsInh_Down 0.00000000 1.000000e+00 0
## 166 LivX_AgvsInh_Down LivX_AgvsInh_Down 1.00000000 1.000000e+00 174
## 167 AhHyd_AgvsInh_Up LivX_AgvsInh_Down 44.05262135 3.160036e-17 14
## 168 AhHyd_AgvsInh_Down LivX_AgvsInh_Down 0.00000000 1.000000e+00 0
## 169 Thyr_AgvsInh_Up AhHyd_AgvsInh_Up 62.28648850 1.874095e-21 16
## 170 Thyr_AgvsInh_Down AhHyd_AgvsInh_Up 0.00000000 1.000000e+00 0
## 171 Ret_AgvsInh_Up AhHyd_AgvsInh_Up 0.00000000 1.000000e+00 0
## 172 Ret_AgvsInh_Down AhHyd_AgvsInh_Up 8.68074512 4.281741e-09 16
## 173 Estr_AgvsInh_Up AhHyd_AgvsInh_Up 0.00000000 1.000000e+00 0
## 174 Estr_AgvsInh_Down AhHyd_AgvsInh_Up 0.00000000 1.000000e+00 0
## 175 Andr_AgvsInh_Up AhHyd_AgvsInh_Up 0.00000000 1.000000e+00 0
## 176 Andr_AgvsInh_Down AhHyd_AgvsInh_Up 35.20775010 3.140510e-02 1
## 177 GC_AgvsInh_Up AhHyd_AgvsInh_Up 34.04870032 1.123432e-16 15
## 178 GC_AgvsInh_Down AhHyd_AgvsInh_Up 0.00000000 1.000000e+00 0
## 179 LivX_AgvsInh_Up AhHyd_AgvsInh_Up 0.77927094 7.261544e-01 1
## 180 LivX_AgvsInh_Down AhHyd_AgvsInh_Up 44.05262135 3.160036e-17 14
## 181 AhHyd_AgvsInh_Up AhHyd_AgvsInh_Up 1.00000000 1.000000e+00 43
## 182 AhHyd_AgvsInh_Down AhHyd_AgvsInh_Up 0.00000000 1.000000e+00 0
## 183 Thyr_AgvsInh_Up AhHyd_AgvsInh_Down 0.00000000 1.000000e+00 0
## 184 Thyr_AgvsInh_Down AhHyd_AgvsInh_Down 3.90710024 4.016461e-05 14
## 185 Ret_AgvsInh_Up AhHyd_AgvsInh_Down 15.45740424 4.985116e-86 147
## 186 Ret_AgvsInh_Down AhHyd_AgvsInh_Down 0.05870611 9.999999e-01 1
## 187 Estr_AgvsInh_Up AhHyd_AgvsInh_Down 0.00000000 1.000000e+00 0
## 188 Estr_AgvsInh_Down AhHyd_AgvsInh_Down 0.00000000 1.000000e+00 0
## 189 Andr_AgvsInh_Up AhHyd_AgvsInh_Down 20.26752689 8.535732e-04 3
## 190 Andr_AgvsInh_Down AhHyd_AgvsInh_Down 0.00000000 1.000000e+00 0
## 191 GC_AgvsInh_Up AhHyd_AgvsInh_Down 0.24426338 9.827396e-01 1
## 192 GC_AgvsInh_Down AhHyd_AgvsInh_Down 15.33456104 1.398295e-09 11
## 193 LivX_AgvsInh_Up AhHyd_AgvsInh_Down 29.90344064 2.029891e-91 101
## 194 LivX_AgvsInh_Down AhHyd_AgvsInh_Down 0.00000000 1.000000e+00 0
## 195 AhHyd_AgvsInh_Up AhHyd_AgvsInh_Down 0.00000000 1.000000e+00 0
## 196 AhHyd_AgvsInh_Down AhHyd_AgvsInh_Down 1.00000000 1.000000e+00 243DotPlot: visualization I select as significant overlaps having an OR > 2 and at least 25 overlapping genes. Dots are shown for PVals < 0.01 (set in the plot). Max value in the plot must be set according to minimum PVal to avoid dots not to be shown.
ResSel <- dplyr::filter(ResMod, OR > 2) %>% dplyr::filter(Numbers > 25)
min(ResSel$Pval)## [1] 5.369891e-272max(ResSel$OR)## [1] 128.8985Dot <- ggplot(ResSel, aes(DEGs, KBase, label=Numbers)) +
geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1)) +
ggtitle('Overlap across AgvsInh-modulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_AgvsInh.pdf'), width=8, height=8)7.3 Visualize overlap results selectively for retinoic, liverX, estrogen, thyroid
Selection
Path <- c('Thyr_AgvsInh_Up', 'Thyr_AgvsInh_Down', 'Ret_AgvsInh_Up', 'Ret_AgvsInh_Down',
'Estr_AgvsInh_Up', 'Estr_AgvsInh_Down', 'LivX_AgvsInh_Up', 'LivX_AgvsInh_Down')
ResPath <- ResSel[ResSel$DEGs %in% Path & ResSel$KBase %in% Path, ]
ResPath
## DEGs KBase OR Pval Numbers
## 1 Ret_AgvsInh_Down Thyr_AgvsInh_Up 4.839574 5.098246e-13 38
## 3 LivX_AgvsInh_Down Thyr_AgvsInh_Up 30.507319 1.560632e-35 35
## 5 LivX_AgvsInh_Up Thyr_AgvsInh_Down 6.680186 1.555239e-17 38
## 7 LivX_AgvsInh_Up Ret_AgvsInh_Up 43.770373 5.369891e-272 346
## 9 Thyr_AgvsInh_Up Ret_AgvsInh_Down 4.839574 5.098246e-13 38
## 11 LivX_AgvsInh_Down Ret_AgvsInh_Down 31.801142 1.312420e-94 115
## 17 Thyr_AgvsInh_Down LivX_AgvsInh_Up 6.680186 1.555239e-17 38
## 18 Ret_AgvsInh_Up LivX_AgvsInh_Up 43.770373 5.369891e-272 346
## 20 Thyr_AgvsInh_Up LivX_AgvsInh_Down 30.507319 1.560632e-35 35
## 21 Ret_AgvsInh_Down LivX_AgvsInh_Down 31.801142 1.312420e-94 115DotPlot: visualization
ResPath <- dplyr::filter(ResPath, OR > 2) %>% dplyr::filter(Numbers > 25)
min(ResPath$Pval)## [1] 5.369891e-272max(ResPath$OR)## [1] 43.77037Dot <- ggplot(ResPath, aes(DEGs, KBase, label=Numbers)) +
geom_point(aes(size=-log10(Pval), col=OR)) +
geom_text() +
scale_size_continuous(range=c(2, 20), limits=c(2, round(-log10(min(ResSel$Pval)) + 0.5))) +
scale_color_viridis_c(limits=c(1, round(max(ResSel$OR)+1)), begin=0.2) + xlab('') + ylab('') +
theme_bw() +
theme(axis.line = element_blank(), axis.title = element_blank(),
axis.text.x = element_text(angle = 45, hjust = 1))+
ggtitle('Overlap across AgvsInh-modulated genes')
Dot
ggsave(Dot, filename=paste0(OutputFolder, 'DotPlot_AgvsInh_Selected.pdf'), width=8, height=8)8. Session info
SessionInfo <- sessionInfo()
Date <- date()Date## [1] "Tue Jul 22 17:29:43 2025"SessionInfo## R version 4.2.1 (2022-06-23)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 20.04.4 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] DESeq2_1.38.3 SummarizedExperiment_1.28.0
## [3] Biobase_2.58.0 MatrixGenerics_1.10.0
## [5] matrixStats_0.63.0 GenomicRanges_1.50.2
## [7] GenomeInfoDb_1.34.9 IRanges_2.32.0
## [9] S4Vectors_0.36.1 BiocGenerics_0.44.0
## [11] GeneOverlap_1.34.0 ggplot2_3.4.1
## [13] dplyr_1.1.0 tidyr_1.3.0
##
## loaded via a namespace (and not attached):
## [1] viridis_0.6.2 httr_1.4.5 sass_0.4.5
## [4] viridisLite_0.4.1 bit64_4.0.5 jsonlite_1.8.4
## [7] gtools_3.9.4 bslib_0.4.2 highr_0.10
## [10] blob_1.2.3 GenomeInfoDbData_1.2.9 yaml_2.3.7
## [13] pillar_1.8.1 RSQLite_2.3.0 lattice_0.20-45
## [16] glue_1.6.2 digest_0.6.31 RColorBrewer_1.1-3
## [19] XVector_0.38.0 colorspace_2.1-0 htmltools_0.5.4
## [22] Matrix_1.5-3 XML_3.99-0.13 pkgconfig_2.0.3
## [25] zlibbioc_1.44.0 purrr_1.0.1 xtable_1.8-4
## [28] scales_1.2.1 BiocParallel_1.32.5 tibble_3.2.1
## [31] annotate_1.76.0 KEGGREST_1.38.0 farver_2.1.1
## [34] generics_0.1.3 cachem_1.0.7 withr_2.5.0
## [37] cli_3.6.1 crayon_1.5.2 magrittr_2.0.3
## [40] memoise_2.0.1 evaluate_0.20 fansi_1.0.4
## [43] gplots_3.1.3 textshaping_0.3.6 tools_4.2.1
## [46] lifecycle_1.0.3 locfit_1.5-9.7 munsell_0.5.0
## [49] DelayedArray_0.24.0 Biostrings_2.66.0 AnnotationDbi_1.60.0
## [52] compiler_4.2.1 jquerylib_0.1.4 systemfonts_1.0.4
## [55] caTools_1.18.2 rlang_1.1.1 grid_4.2.1
## [58] RCurl_1.98-1.10 rstudioapi_0.14 labeling_0.4.2
## [61] bitops_1.0-7 rmarkdown_2.20 gtable_0.3.1
## [64] codetools_0.2-19 DBI_1.1.3 R6_2.5.1
## [67] gridExtra_2.3 knitr_1.42 fastmap_1.1.1
## [70] bit_4.0.5 utf8_1.2.3 ragg_1.2.3
## [73] KernSmooth_2.23-20 parallel_4.2.1 Rcpp_1.0.10
## [76] png_0.1-8 vctrs_0.6.2 geneplotter_1.76.0
## [79] tidyselect_1.2.0 xfun_0.37