Annotation of Murase et al. escapee CpGs
Gaja Matassa
Date: May 05, 2025
1. Environment setting
library(plotly)
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library(ggplot2)
library(dplyr)
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library(scales)
library(gridExtra)
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library(ChIPseeker)
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## ChIPseeker v1.34.1 For help: https://guangchuangyu.github.io/software/ChIPseeker
##
## If you use ChIPseeker in published research, please cite:
## Qianwen Wang, Ming Li, Tianzhi Wu, Li Zhan, Lin Li, Meijun Chen, Wenqin Xie, Zijing Xie, Erqiang Hu, Shuangbin Xu, Guangchuang Yu. Exploring epigenomic datasets by ChIPseeker. Current Protocols 2022, 2(10): e585
library(org.Hs.eg.db)
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library(AnnotationDbi)
library(RColorBrewer)
library(viridis)
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library(topGO)
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source("../5.DMRInterpretation/TopGO/TopGO_helper_meth.R")
GTFFile <- "~/DataDir/3.TwistBedAnn/Input/gencode.v35.annotation.gtf.gz"
txdb_v35 <- GenomicFeatures::makeTxDbFromGFF(GTFFile, format="gtf")
## Import genomic features from the file as a GRanges object ...
## OK
## Prepare the 'metadata' data frame ... OK
## Make the TxDb object ...
## Warning in .get_cds_IDX(mcols0$type, mcols0$phase): The "phase" metadata column contains non-NA values for features of type
## stop_codon. This information was ignored.
## OKInputFolder <- params$InputFolder
OutputFolder <- params$OutputFolder2. Loading data
2.1 BSSeq object
Loading of bsseq object of escapees generated in 2.Exploration_escapees.Rmd
bsseq_obj_escapees <- readRDS(paste0(params$InputFolder, "bsseq_obj_escapees_Murase.rds"))2.2 Gene universe (genes annotated to twist bait regions)
TwistAnnotated <- readRDS(params$TwistAnnotated)
TwistAnnotated %>% head()
## seqnames start end width strand
## 1 chr1 10466 10585 120 *
## 2 chr1 10790 10909 120 *
## 3 chr1 15806 15925 120 *
## 4 chr1 18768 18887 120 *
## 5 chr1 29357 29476 120 *
## 6 chr1 36544 36663 120 *
## ann
## 1 cg14817997,cpg_inter
## 2 cg16269199,cg26928153,cpg_inter
## 3 CTCF_binding_site,cg13869341,cpg_inter,promoter_flanking_region
## 4 cg14008030,cpg_inter
## 5 cg12045430,cg20826792,cpg_islands,promoter
## 6 cg18231760,cpg_inter,promoter_flanking_region
## annotation geneChr geneStart geneEnd geneLength geneStrand
## 1 Promoter (1-2kb) 1 11869 14409 2541 1
## 2 Promoter (<=1kb) 1 11869 14409 2541 1
## 3 Promoter (1-2kb) 1 17369 17436 68 2
## 4 Promoter (1-2kb) 1 17369 17436 68 2
## 5 Promoter (<=1kb) 1 29554 31097 1544 1
## 6 Promoter (<=1kb) 1 34554 36081 1528 2
## ensembl_gene_id_version transcriptId distanceToTSS
## 1 ENSG00000223972.5 ENST00000456328.2 -1284
## 2 ENSG00000223972.5 ENST00000456328.2 -960
## 3 ENSG00000278267.1 ENST00000619216.1 1511
## 4 ENSG00000278267.1 ENST00000619216.1 -1332
## 5 ENSG00000243485.5 ENST00000473358.1 -78
## 6 ENSG00000237613.2 ENST00000417324.1 -463
## flank_txIds
## 1 ENST00000456328.2;ENST00000450305.2;ENST00000488147.1
## 2 ENST00000456328.2;ENST00000450305.2;ENST00000488147.1
## 3 ENST00000456328.2;ENST00000450305.2;ENST00000488147.1;ENST00000619216.1
## 4 ENST00000456328.2;ENST00000488147.1;ENST00000619216.1
## 5 ENST00000488147.1;ENST00000473358.1;ENST00000469289.1;ENST00000607096.1
## 6 ENST00000417324.1;ENST00000461467.1
## flank_geneIds
## 1 ENSG00000223972.5;ENSG00000223972.5;ENSG00000227232.5
## 2 ENSG00000223972.5;ENSG00000223972.5;ENSG00000227232.5
## 3 ENSG00000223972.5;ENSG00000223972.5;ENSG00000227232.5;ENSG00000278267.1
## 4 ENSG00000223972.5;ENSG00000227232.5;ENSG00000278267.1
## 5 ENSG00000227232.5;ENSG00000243485.5;ENSG00000243485.5;ENSG00000284332.1
## 6 ENSG00000237613.2;ENSG00000237613.2
## flank_gene_distances ensembl_gene_id hgnc_symbol external_gene_name
## 1 -1284;-1425;0 ENSG00000223972 DDX11L1 DDX11L1
## 2 -960;-1101;0 ENSG00000223972 DDX11L1 DDX11L1
## 3 3937;3796;0;1511 ENSG00000278267 MIR6859-1 MIR6859-1
## 4 6899;0;-1332 ENSG00000278267 MIR6859-1 MIR6859-1
## 5 0;-78;-791;-890 ENSG00000243485 MIR1302-2HG MIR1302-2HG
## 6 -463;-471 ENSG00000237613 FAM138A FAM138A
## gene_biotype
## 1 transcribed_unprocessed_pseudogene
## 2 transcribed_unprocessed_pseudogene
## 3 miRNA
## 4 miRNA
## 5 lncRNA
## 6 lncRNA
## description
## 1 DEAD/H-box helicase 11 like 1 (pseudogene) [Source:HGNC Symbol;Acc:HGNC:37102]
## 2 DEAD/H-box helicase 11 like 1 (pseudogene) [Source:HGNC Symbol;Acc:HGNC:37102]
## 3 microRNA 6859-1 [Source:HGNC Symbol;Acc:HGNC:50039]
## 4 microRNA 6859-1 [Source:HGNC Symbol;Acc:HGNC:50039]
## 5 MIR1302-2 host gene [Source:HGNC Symbol;Acc:HGNC:52482]
## 6 family with sequence similarity 138 member A [Source:HGNC Symbol;Acc:HGNC:32334]
## chromosome_name start_position end_position
## 1 1 11869 14409
## 2 1 11869 14409
## 3 1 17369 17436
## 4 1 17369 17436
## 5 1 29554 31109
## 6 1 34554 36081Genes_df <- TwistAnnotated[, c("ensembl_gene_id_version", "ensembl_gene_id", "hgnc_symbol", "gene_biotype")] %>% dplyr::distinct()%>%filter(!is.na(hgnc_symbol))%>%filter(!hgnc_symbol%in%"")
rownames(Genes_df) <- NULLThese are the genes with the same symbol but different ensembl id
Genes_df[Genes_df$hgnc_symbol%in%Genes_df[duplicated(Genes_df$hgnc_symbol), "hgnc_symbol"],]
## ensembl_gene_id_version ensembl_gene_id hgnc_symbol
## 3309 ENSG00000285053.1 ENSG00000285053 TBCE
## 3310 ENSG00000284770.2 ENSG00000284770 TBCE
## 20449 ENSG00000237940.3 ENSG00000237940 LINC01238
## 20451 ENSG00000261186.2 ENSG00000261186 LINC01238
## 21924 ENSG00000206195.11 ENSG00000206195 DUXAP8
## 21926 ENSG00000271672.1 ENSG00000271672 DUXAP8
## 24581 ENSG00000284862.3 ENSG00000284862 CCDC39
## 24582 ENSG00000145075.13 ENSG00000145075 CCDC39
## 30308 ENSG00000272655.2 ENSG00000272655 POLR2J4
## 30309 ENSG00000214783.9 ENSG00000214783 POLR2J4
## gene_biotype
## 3309 protein_coding
## 3310 protein_coding
## 20449 lncRNA
## 20451 lncRNA
## 21924 lncRNA
## 21926 transcribed_processed_pseudogene
## 24581 protein_coding
## 24582 lncRNA
## 30308 transcribed_unprocessed_pseudogene
## 30309 lncRNAGenes_df$entrez_gene_id <- as.vector(mapIds(org.Hs.eg.db, Genes_df$hgnc_symbol, column = "ENTREZID", keytype = "SYMBOL"))
## 'select()' returned 1:many mapping between keys and columnsnrow(Genes_df[is.na(Genes_df$entrez_gene_id),]) #number of genes without an entrez id
## [1] 421GeneUniverse_symbol <- unique(Genes_df$hgnc_symbol)
GeneUniverse_entrezid <- na.omit(unique(Genes_df$entrez_gene_id))3. Escapee CpG annotation and visualization with
ChIPseeker
CpGs are now annotated to their associated genes and genomic regions
using the annotatePeaks function of the
ChIPseekerR package, using a TxDb object. The GenomicFeatures
package uses TxDb objects to store transcript metadata.
This class maps the 5’ and 3’ untranslated regions (UTRs), protein
coding sequences (CDSs) and exons for a set of mRNA transcripts to their
associated genome. All TxDb objects are backed by a SQLite
database that manages genomic locations and the relationships between
pre-processed mRNA transcripts, exons, protein coding sequences, and
their related gene identifiers.
TxDb created by us
Remember that bsseq_obj_escapees (and bsseq_obj_NonEscapees) have 1-based positions
bsseq_obj_escapees
## Loading required package: bsseq
## Loading required package: GenomicRanges
## Loading required package: GenomeInfoDb
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## An object of type 'BSseq' with
## 207478 methylation loci
## 14 samples
## has not been smoothed
## All assays are in-memorygranges(bsseq_obj_escapees)
## GRanges object with 207478 ranges and 0 metadata columns:
## seqnames ranges strand
## <Rle> <IRanges> <Rle>
## [1] chr1 10469 *
## [2] chr1 10471 *
## [3] chr1 10484 *
## [4] chr1 10489 *
## [5] chr1 10493 *
## ... ... ... ...
## [207474] chrM 11647 *
## [207475] chrM 11689 *
## [207476] chrM 11692 *
## [207477] chrM 11710 *
## [207478] chrM 11716 *
## -------
## seqinfo: 25 sequences from an unspecified genome; no seqlengthsEscapeeAnno <- annotatePeak(
granges(bsseq_obj_escapees),
tssRegion = c(-3000, 3000),
TxDb = txdb_v35,
level = "transcript", #level = "gene"
assignGenomicAnnotation = TRUE,
genomicAnnotationPriority = c("Promoter", "5UTR", "3UTR", "Exon", "Intron",
"Downstream", "Intergenic"),
overlap = "TSS",
verbose = TRUE,
columns = c("ENTREZID", "ENSEMBL", "SYMBOL", "GENENAME")
)
## >> preparing features information... 2025-05-05 11:01:37 AM
## >> identifying nearest features... 2025-05-05 11:01:38 AM
## >> calculating distance from peak to TSS... 2025-05-05 11:01:40 AM
## >> assigning genomic annotation... 2025-05-05 11:01:40 AM
## >> assigning chromosome lengths 2025-05-05 11:02:06 AM
## >> done... 2025-05-05 11:02:06 AMChIPseeker::plotAnnoBar(EscapeeAnno)
ChIPseeker::plotAnnoPie(EscapeeAnno)
ChIPseeker::vennpie(EscapeeAnno)
ChIPseeker::plotDistToTSS(EscapeeAnno)
From ensembl ids to gene symbols, entrez ids and metadata
Host <- "https://aug2020.archive.ensembl.org"
Specie <- "hsapiens"
BioMart <- biomaRt::listMarts(host=Host)[1,1]
Version <- biomaRt::listMarts(host=Host)[1,2]
Mart <- biomaRt::useMart(host=Host, biomart=BioMart, version=Version,
dataset=paste0(Specie,'_gene_ensembl'))
EscapeeGenes_ensembl = unique(as.data.frame(EscapeeAnno)$geneId) #Genes assigned to the escapees regions by chipseeker
Attributes = c("ensembl_gene_id_version", "ensembl_gene_id", "hgnc_symbol", "gene_biotype")
EscapeeGeneAnnotation <- biomaRt::getBM(mart=Mart, filters='ensembl_gene_id_version', values=EscapeeGenes_ensembl, attributes=Attributes, uniqueRows=TRUE)
EscapeeGeneAnnotation <- EscapeeGeneAnnotation %>% dplyr::distinct() #%>%filter(!is.na(hgnc_symbol)) %>% filter(!hgnc_symbol%in%"")EscapeeGenes_ensembl[!EscapeeGenes_ensembl %in% EscapeeGeneAnnotation$ensembl_gene_id_version] %>% head() #ChipSeeker annotation that are not present in the biomart
## character(0)
EscapeeGenes_symbol = EscapeeGeneAnnotation %>% filter(!is.na(hgnc_symbol)) %>% filter(!hgnc_symbol%in%"") %>% pull(hgnc_symbol) %>% unique()
EscapeeGenes_entrez = mapIds(org.Hs.eg.db, keys = EscapeeGenes_symbol, column = "ENTREZID", keytype = "SYMBOL") %>% unique()
## 'select()' returned 1:many mapping between keys and columnsAnnotatedEscapees <- dplyr::left_join(as.data.frame(EscapeeAnno), EscapeeGeneAnnotation, by=c('geneId' = 'ensembl_gene_id_version'))
## Warning in dplyr::left_join(as.data.frame(EscapeeAnno), EscapeeGeneAnnotation, : Detected an unexpected many-to-many relationship between `x` and `y`.
## ℹ Row 108573 of `x` matches multiple rows in `y`.
## ℹ Row 2467 of `y` matches multiple rows in `x`.
## ℹ If a many-to-many relationship is expected, set `relationship =
## "many-to-many"` to silence this warning.4. Functional enrichment analysis
4.1 Selection of modulated genes and generation of gene vector
GeneVectors <- topGOGeneVectors_meth_v2(gene_symbols = EscapeeGenes_symbol, genomic_type = "all", gene_type = "all", Universe = GeneUniverse_symbol) %>% unlist()
## [1] "All genomic regions and gene types will be kept"
## [1] "There are some genes symbols which are not in the gene universe! They will not be considered..."Genes associated to escapee CpGs that are not present in the universe:
not_present <- EscapeeGeneAnnotation %>% filter(hgnc_symbol %in% unique(na.omit(EscapeeGenes_symbol))[!unique(na.omit(EscapeeGenes_symbol)) %in% GeneUniverse_symbol])
not_present## ensembl_gene_id_version ensembl_gene_id hgnc_symbol gene_biotype
## 1 ENSG00000203897.4 ENSG00000203897 SPATA42 lncRNA
## 2 ENSG00000206552.4 ENSG00000206552 KRBOX1-AS1 lncRNA
## 3 ENSG00000226960.1 ENSG00000226960 MTCO1P21 unprocessed_pseudogene
## 4 ENSG00000248527.1 ENSG00000248527 MTATP6P1 unprocessed_pseudogene
## 5 ENSG00000124610.5 ENSG00000124610 H1-1 protein_coding
## 6 ENSG00000146047.7 ENSG00000146047 H2BC1 protein_coding
## 7 ENSG00000234816.2 ENSG00000234816 H2AC5P unprocessed_pseudogene
## 8 ENSG00000245729.2 ENSG00000245729 LINC02226 lncRNA
## 9 ENSG00000247627.2 ENSG00000247627 MTND4P12 processed_pseudogene
## 10 ENSG00000278970.2 ENSG00000278970 HEIH lncRNA
## 11 ENSG00000189398.5 ENSG00000189398 OR7E12P unprocessed_pseudogene
## 12 ENSG00000199069.3 ENSG00000199069 MIR323A miRNA
## 13 ENSG00000201679.1 ENSG00000201679 SNORD115-15 snoRNA
## 14 ENSG00000202261.1 ENSG00000202261 SNORD115-44 snoRNA
## 15 ENSG00000206609.1 ENSG00000206609 SNORD116-11 snoRNA
## 16 ENSG00000206855.1 ENSG00000206855 RNU6-571P snRNA
## 17 ENSG00000207001.1 ENSG00000207001 SNORD116-2 snoRNA
## 18 ENSG00000207197.1 ENSG00000207197 SNORD116-12 snoRNA
## 19 ENSG00000207279.1 ENSG00000207279 SNORD116-24 snoRNA
## 20 ENSG00000207442.1 ENSG00000207442 SNORD116-6 snoRNA
## 21 ENSG00000207754.3 ENSG00000207754 MIR487B miRNA
## 22 ENSG00000207942.2 ENSG00000207942 MIR136 miRNA
## 23 ENSG00000221745.3 ENSG00000221745 MIR1197 miRNA
## 24 ENSG00000230417.12 ENSG00000230417 LINC00856 lncRNA
## 25 ENSG00000236937.2 ENSG00000236937 PTGES3P4 processed_pseudogene
## 26 ENSG00000255417.1 ENSG00000255417 MTCO2P15 processed_pseudogene
## 27 ENSG00000197134.13 ENSG00000197134 ZNF257 protein_coding
## 28 ENSG00000198899.2 ENSG00000198899 MT-ATP6 protein_coding
## 29 ENSG00000210107.1 ENSG00000210107 MT-TQ Mt_tRNA
## 30 ENSG00000210112.1 ENSG00000210112 MT-TM Mt_tRNA
## 31 ENSG00000216195.3 ENSG00000216195 MIR941-4 miRNA
## 32 ENSG00000235590.7 ENSG00000235590 GNAS-AS1 lncRNA
## 33 ENSG00000237206.1 ENSG00000237206 IMPDH1P4 processed_pseudogene
## 34 ENSG00000273148.1 ENSG00000273148 LINC00653 lncRNA
## 35 ENSG00000284585.1 ENSG00000284585 MIR4722 miRNAThese are the CpGs annotated with those genes
EscapeeAnno@anno %>% as.data.frame() %>% filter(geneId %in% not_present$ensembl_gene_id_version)
## seqnames start end width strand
## 1 chr1 633816 633816 1 *
## 2 chr1 633891 633891 1 *
## 3 chr1 633950 633950 1 *
## 4 chr1 634024 634024 1 *
## 5 chr1 634028 634028 1 *
## 6 chr1 93927989 93927989 1 *
## 7 chr1 108857482 108857482 1 *
## 8 chr1 108857496 108857496 1 *
## 9 chr1 108857523 108857523 1 *
## 10 chr3 42936688 42936688 1 *
## 11 chr3 42936752 42936752 1 *
## 12 chr3 42936756 42936756 1 *
## 13 chr3 42936781 42936781 1 *
## 14 chr3 42936787 42936787 1 *
## 15 chr5 8457546 8457546 1 *
## 16 chr5 134927319 134927319 1 *
## 17 chr5 134927361 134927361 1 *
## 18 chr5 134927373 134927373 1 *
## 19 chr5 134927406 134927406 1 *
## 20 chr5 134927443 134927443 1 *
## 21 chr5 180830679 180830679 1 *
## 22 chr5 180830691 180830691 1 *
## 23 chr5 180830697 180830697 1 *
## 24 chr5 180830795 180830795 1 *
## 25 chr5 180830797 180830797 1 *
## 26 chr6 25726684 25726684 1 *
## 27 chr6 25726719 25726719 1 *
## 28 chr6 25726723 25726723 1 *
## 29 chr6 25726725 25726725 1 *
## 30 chr6 25726728 25726728 1 *
## 31 chr6 25726739 25726739 1 *
## 32 chr6 25726754 25726754 1 *
## 33 chr6 25726791 25726791 1 *
## 34 chr6 25726879 25726879 1 *
## 35 chr6 25726886 25726886 1 *
## 36 chr6 25726913 25726913 1 *
## 37 chr6 25726968 25726968 1 *
## 38 chr6 25726999 25726999 1 *
## 39 chr6 25727011 25727011 1 *
## 40 chr6 25727063 25727063 1 *
## 41 chr6 25727081 25727081 1 *
## 42 chr6 25727109 25727109 1 *
## 43 chr6 25727128 25727128 1 *
## 44 chr6 25727135 25727135 1 *
## 45 chr6 25727139 25727139 1 *
## 46 chr6 25727149 25727149 1 *
## 47 chr6 25727170 25727170 1 *
## 48 chr6 26018542 26018542 1 *
## 49 chr6 26018551 26018551 1 *
## 50 chr6 26018614 26018614 1 *
## 51 chr6 26018621 26018621 1 *
## 52 chr6 26018639 26018639 1 *
## 53 chr6 26018645 26018645 1 *
## 54 chr6 26018703 26018703 1 *
## 55 chr6 26018807 26018807 1 *
## 56 chr6 26018864 26018864 1 *
## 57 chr6 26043942 26043942 1 *
## 58 chr6 26043976 26043976 1 *
## 59 chr6 26043992 26043992 1 *
## 60 chr6 26044001 26044001 1 *
## 61 chr6 26044005 26044005 1 *
## 62 chr6 26044037 26044037 1 *
## 63 chr6 26044040 26044040 1 *
## 64 chr6 26044046 26044046 1 *
## 65 chr6 26044076 26044076 1 *
## 66 chr6 26044088 26044088 1 *
## 67 chr6 26044110 26044110 1 *
## 68 chr6 26044114 26044114 1 *
## 69 chr6 26044120 26044120 1 *
## 70 chr6 26044125 26044125 1 *
## 71 chr6 26044150 26044150 1 *
## 72 chr6 26044153 26044153 1 *
## 73 chr6 26044177 26044177 1 *
## 74 chr6 26044184 26044184 1 *
## 75 chr6 26044196 26044196 1 *
## 76 chr6 26044211 26044211 1 *
## 77 chr6 26044232 26044232 1 *
## 78 chr6 26044237 26044237 1 *
## 79 chr6 26044240 26044240 1 *
## 80 chr6 26044267 26044267 1 *
## 81 chr6 26044288 26044288 1 *
## 82 chr6 26044309 26044309 1 *
## 83 chr6 26044336 26044336 1 *
## 84 chr6 26044375 26044375 1 *
## 85 chr6 26044393 26044393 1 *
## 86 chr6 26044409 26044409 1 *
## 87 chr10 68912571 68912571 1 *
## 88 chr10 78247466 78247466 1 *
## 89 chr10 78247514 78247514 1 *
## 90 chr10 78247817 78247817 1 *
## 91 chr10 78247982 78247982 1 *
## 92 chr10 78248260 78248260 1 *
## 93 chr10 78269819 78269819 1 *
## 94 chr10 78269871 78269871 1 *
## 95 chr10 78269878 78269878 1 *
## 96 chr10 78299846 78299846 1 *
## 97 chr10 78299853 78299853 1 *
## 98 chr10 102845550 102845550 1 *
## 99 chr10 102845571 102845571 1 *
## 100 chr11 3387615 3387615 1 *
## 101 chr11 103403924 103403924 1 *
## 102 chr14 100884641 100884641 1 *
## 103 chr14 100884664 100884664 1 *
## 104 chr14 100884678 100884678 1 *
## 105 chr14 100884681 100884681 1 *
## 106 chr14 100884684 100884684 1 *
## 107 chr14 101025332 101025332 1 *
## 108 chr14 101025406 101025406 1 *
## 109 chr14 101025480 101025480 1 *
## 110 chr14 101025502 101025502 1 *
## 111 chr14 101025560 101025560 1 *
## 112 chr14 101025585 101025585 1 *
## 113 chr14 101025604 101025604 1 *
## 114 chr14 101025618 101025618 1 *
## 115 chr14 101025657 101025657 1 *
## 116 chr14 101025694 101025694 1 *
## 117 chr14 101025722 101025722 1 *
## 118 chr14 101025755 101025755 1 *
## 119 chr14 101025760 101025760 1 *
## 120 chr14 101025762 101025762 1 *
## 121 chr14 101025766 101025766 1 *
## 122 chr14 101025780 101025780 1 *
## 123 chr14 101046742 101046742 1 *
## 124 chr14 101046750 101046750 1 *
## 125 chr15 25055496 25055496 1 *
## 126 chr15 25064951 25064951 1 *
## 127 chr15 25064974 25064974 1 *
## 128 chr15 25075950 25075950 1 *
## 129 chr15 25076074 25076074 1 *
## 130 chr15 25076981 25076981 1 *
## 131 chr15 25076984 25076984 1 *
## 132 chr15 25093921 25093921 1 *
## 133 chr15 25093937 25093937 1 *
## 134 chr15 25197549 25197549 1 *
## 135 chr15 25197580 25197580 1 *
## 136 chr15 25251255 25251255 1 *
## 137 chr15 25251358 25251358 1 *
## 138 chr15 25251415 25251415 1 *
## 139 chr15 25251456 25251456 1 *
## 140 chr15 25251461 25251461 1 *
## 141 chr16 88716474 88716474 1 *
## 142 chr16 88716502 88716502 1 *
## 143 chr16 88716554 88716554 1 *
## 144 chr19 22052414 22052414 1 *
## 145 chr19 22052429 22052429 1 *
## 146 chr19 22052443 22052443 1 *
## 147 chr19 22052454 22052454 1 *
## 148 chr19 22052470 22052470 1 *
## 149 chr19 22052479 22052479 1 *
## 150 chr19 22052495 22052495 1 *
## 151 chr19 22052505 22052505 1 *
## 152 chr19 22052519 22052519 1 *
## 153 chr19 22052607 22052607 1 *
## 154 chr19 22052652 22052652 1 *
## 155 chr19 22052699 22052699 1 *
## 156 chr19 22052707 22052707 1 *
## 157 chr19 22052745 22052745 1 *
## 158 chr19 22052749 22052749 1 *
## 159 chr19 22052769 22052769 1 *
## 160 chr19 22052775 22052775 1 *
## 161 chr19 22052799 22052799 1 *
## 162 chr20 18794489 18794489 1 *
## 163 chr20 58850954 58850954 1 *
## 164 chr20 58850999 58850999 1 *
## 165 chr20 58851002 58851002 1 *
## 166 chr20 58851011 58851011 1 *
## 167 chr20 58851076 58851076 1 *
## 168 chr20 58851083 58851083 1 *
## 169 chr20 58851160 58851160 1 *
## 170 chr20 58851185 58851185 1 *
## 171 chr20 58851209 58851209 1 *
## 172 chr20 58851219 58851219 1 *
## 173 chr20 58851226 58851226 1 *
## 174 chr20 58851267 58851267 1 *
## 175 chr20 58851313 58851313 1 *
## 176 chr20 58851319 58851319 1 *
## 177 chr20 58851328 58851328 1 *
## 178 chr20 58851336 58851336 1 *
## 179 chr20 58851340 58851340 1 *
## 180 chr20 63919800 63919800 1 *
## 181 chr20 63919806 63919806 1 *
## 182 chrX 43279610 43279610 1 *
## 183 chrX 43279616 43279616 1 *
## 184 chrM 4375 4375 1 *
## 185 chrM 4426 4426 1 *
## 186 chrM 8722 8722 1 *
## 187 chrM 8781 8781 1 *
## 188 chrM 8855 8855 1 *
## annotation geneChr
## 1 Promoter (<=1kb) 1
## 2 Promoter (<=1kb) 1
## 3 Promoter (<=1kb) 1
## 4 Promoter (<=1kb) 1
## 5 Promoter (<=1kb) 1
## 6 Promoter (<=1kb) 1
## 7 Promoter (<=1kb) 1
## 8 Promoter (<=1kb) 1
## 9 Promoter (<=1kb) 1
## 10 Promoter (<=1kb) 3
## 11 Promoter (<=1kb) 3
## 12 Promoter (<=1kb) 3
## 13 Promoter (<=1kb) 3
## 14 Promoter (<=1kb) 3
## 15 Promoter (<=1kb) 5
## 16 Promoter (<=1kb) 5
## 17 Promoter (<=1kb) 5
## 18 Promoter (<=1kb) 5
## 19 Promoter (<=1kb) 5
## 20 Promoter (<=1kb) 5
## 21 Promoter (<=1kb) 5
## 22 Promoter (<=1kb) 5
## 23 Promoter (<=1kb) 5
## 24 Promoter (<=1kb) 5
## 25 Promoter (<=1kb) 5
## 26 Promoter (<=1kb) 6
## 27 Promoter (<=1kb) 6
## 28 Promoter (<=1kb) 6
## 29 Promoter (<=1kb) 6
## 30 Promoter (<=1kb) 6
## 31 Promoter (<=1kb) 6
## 32 Promoter (<=1kb) 6
## 33 Promoter (<=1kb) 6
## 34 Promoter (<=1kb) 6
## 35 Promoter (<=1kb) 6
## 36 Promoter (<=1kb) 6
## 37 Promoter (<=1kb) 6
## 38 Promoter (<=1kb) 6
## 39 Promoter (<=1kb) 6
## 40 Promoter (<=1kb) 6
## 41 Promoter (<=1kb) 6
## 42 Promoter (<=1kb) 6
## 43 Promoter (<=1kb) 6
## 44 Promoter (<=1kb) 6
## 45 Promoter (<=1kb) 6
## 46 Promoter (<=1kb) 6
## 47 Promoter (<=1kb) 6
## 48 Promoter (<=1kb) 6
## 49 Promoter (<=1kb) 6
## 50 Promoter (<=1kb) 6
## 51 Promoter (<=1kb) 6
## 52 Promoter (<=1kb) 6
## 53 Promoter (<=1kb) 6
## 54 Promoter (<=1kb) 6
## 55 Promoter (1-2kb) 6
## 56 Promoter (1-2kb) 6
## 57 Promoter (<=1kb) 6
## 58 Promoter (<=1kb) 6
## 59 Promoter (<=1kb) 6
## 60 Promoter (<=1kb) 6
## 61 Promoter (<=1kb) 6
## 62 Promoter (<=1kb) 6
## 63 Promoter (<=1kb) 6
## 64 Promoter (<=1kb) 6
## 65 Promoter (<=1kb) 6
## 66 Promoter (<=1kb) 6
## 67 Promoter (<=1kb) 6
## 68 Promoter (<=1kb) 6
## 69 Promoter (<=1kb) 6
## 70 Promoter (<=1kb) 6
## 71 Promoter (<=1kb) 6
## 72 Promoter (<=1kb) 6
## 73 Promoter (<=1kb) 6
## 74 Promoter (<=1kb) 6
## 75 Promoter (<=1kb) 6
## 76 Promoter (<=1kb) 6
## 77 Promoter (<=1kb) 6
## 78 Promoter (<=1kb) 6
## 79 Promoter (<=1kb) 6
## 80 Promoter (<=1kb) 6
## 81 Promoter (<=1kb) 6
## 82 Promoter (<=1kb) 6
## 83 Promoter (<=1kb) 6
## 84 Promoter (<=1kb) 6
## 85 Promoter (<=1kb) 6
## 86 Promoter (<=1kb) 6
## 87 Promoter (<=1kb) 10
## 88 Promoter (1-2kb) 10
## 89 Promoter (1-2kb) 10
## 90 Promoter (<=1kb) 10
## 91 Promoter (<=1kb) 10
## 92 Promoter (<=1kb) 10
## 93 Promoter (2-3kb) 10
## 94 Promoter (2-3kb) 10
## 95 Promoter (2-3kb) 10
## 96 Promoter (1-2kb) 10
## 97 Promoter (1-2kb) 10
## 98 Promoter (<=1kb) 10
## 99 Promoter (<=1kb) 10
## 100 Intron (ENST00000529482.5/ENSG00000223756.7, intron 3 of 8) 11
## 101 Promoter (<=1kb) 11
## 102 Promoter (<=1kb) 14
## 103 Promoter (<=1kb) 14
## 104 Promoter (<=1kb) 14
## 105 Promoter (<=1kb) 14
## 106 Promoter (<=1kb) 14
## 107 Promoter (<=1kb) 14
## 108 Promoter (<=1kb) 14
## 109 Promoter (<=1kb) 14
## 110 Promoter (<=1kb) 14
## 111 Promoter (<=1kb) 14
## 112 Promoter (<=1kb) 14
## 113 Promoter (<=1kb) 14
## 114 Promoter (<=1kb) 14
## 115 Promoter (<=1kb) 14
## 116 Promoter (<=1kb) 14
## 117 Promoter (<=1kb) 14
## 118 Promoter (<=1kb) 14
## 119 Promoter (<=1kb) 14
## 120 Promoter (<=1kb) 14
## 121 Promoter (<=1kb) 14
## 122 Promoter (<=1kb) 14
## 123 Promoter (<=1kb) 14
## 124 Promoter (<=1kb) 14
## 125 Promoter (1-2kb) 15
## 126 Promoter (<=1kb) 15
## 127 Promoter (<=1kb) 15
## 128 Promoter (<=1kb) 15
## 129 Promoter (<=1kb) 15
## 130 Promoter (<=1kb) 15
## 131 Promoter (<=1kb) 15
## 132 Promoter (<=1kb) 15
## 133 Promoter (<=1kb) 15
## 134 Promoter (<=1kb) 15
## 135 Promoter (<=1kb) 15
## 136 Promoter (<=1kb) 15
## 137 Promoter (<=1kb) 15
## 138 Promoter (<=1kb) 15
## 139 Promoter (<=1kb) 15
## 140 Promoter (<=1kb) 15
## 141 Promoter (<=1kb) 16
## 142 Promoter (<=1kb) 16
## 143 Promoter (<=1kb) 16
## 144 Promoter (<=1kb) 19
## 145 Promoter (<=1kb) 19
## 146 Promoter (<=1kb) 19
## 147 Promoter (<=1kb) 19
## 148 Promoter (<=1kb) 19
## 149 Promoter (<=1kb) 19
## 150 Promoter (<=1kb) 19
## 151 Promoter (<=1kb) 19
## 152 Promoter (<=1kb) 19
## 153 Promoter (<=1kb) 19
## 154 Promoter (<=1kb) 19
## 155 Promoter (<=1kb) 19
## 156 Promoter (<=1kb) 19
## 157 Promoter (<=1kb) 19
## 158 Promoter (<=1kb) 19
## 159 Promoter (<=1kb) 19
## 160 Promoter (<=1kb) 19
## 161 Promoter (<=1kb) 19
## 162 Promoter (<=1kb) 20
## 163 Promoter (<=1kb) 20
## 164 Promoter (<=1kb) 20
## 165 Promoter (<=1kb) 20
## 166 Promoter (<=1kb) 20
## 167 Promoter (<=1kb) 20
## 168 Promoter (<=1kb) 20
## 169 Promoter (<=1kb) 20
## 170 Promoter (<=1kb) 20
## 171 Promoter (<=1kb) 20
## 172 Promoter (<=1kb) 20
## 173 Promoter (<=1kb) 20
## 174 Promoter (<=1kb) 20
## 175 Promoter (<=1kb) 20
## 176 Promoter (<=1kb) 20
## 177 Promoter (<=1kb) 20
## 178 Promoter (<=1kb) 20
## 179 Promoter (<=1kb) 20
## 180 Promoter (<=1kb) 20
## 181 Promoter (<=1kb) 20
## 182 Promoter (<=1kb) 23
## 183 Promoter (<=1kb) 23
## 184 Promoter (<=1kb) 25
## 185 Promoter (<=1kb) 25
## 186 Promoter (<=1kb) 25
## 187 Promoter (<=1kb) 25
## 188 Promoter (<=1kb) 25
## geneStart geneEnd geneLength geneStrand geneId
## 1 633696 634376 681 1 ENSG00000248527.1
## 2 633696 634376 681 1 ENSG00000248527.1
## 3 633696 634376 681 1 ENSG00000248527.1
## 4 633696 634376 681 1 ENSG00000248527.1
## 5 633696 634376 681 1 ENSG00000248527.1
## 6 93927714 93928302 589 2 ENSG00000226960.1
## 7 108857244 108858340 1097 1 ENSG00000203897.4
## 8 108857244 108858340 1097 1 ENSG00000203897.4
## 9 108857244 108858340 1097 1 ENSG00000203897.4
## 10 42934252 42936785 2534 2 ENSG00000206552.4
## 11 42934252 42936785 2534 2 ENSG00000206552.4
## 12 42934252 42936785 2534 2 ENSG00000206552.4
## 13 42934252 42936785 2534 2 ENSG00000206552.4
## 14 42934252 42936785 2534 2 ENSG00000206552.4
## 15 8333481 8457558 124078 2 ENSG00000245729.2
## 16 134926660 134928036 1377 2 ENSG00000247627.2
## 17 134926660 134928036 1377 2 ENSG00000247627.2
## 18 134926660 134928036 1377 2 ENSG00000247627.2
## 19 134926660 134928036 1377 2 ENSG00000247627.2
## 20 134926660 134928036 1377 2 ENSG00000247627.2
## 21 180826871 180830659 3789 2 ENSG00000278970.2
## 22 180826871 180830659 3789 2 ENSG00000278970.2
## 23 180826871 180830659 3789 2 ENSG00000278970.2
## 24 180826871 180830659 3789 2 ENSG00000278970.2
## 25 180826871 180830659 3789 2 ENSG00000278970.2
## 26 25726777 25727345 569 1 ENSG00000146047.7
## 27 25726777 25727345 569 1 ENSG00000146047.7
## 28 25726777 25727345 569 1 ENSG00000146047.7
## 29 25726777 25727345 569 1 ENSG00000146047.7
## 30 25726777 25727345 569 1 ENSG00000146047.7
## 31 25726777 25727345 569 1 ENSG00000146047.7
## 32 25726777 25727345 569 1 ENSG00000146047.7
## 33 25726777 25727345 569 1 ENSG00000146047.7
## 34 25726777 25727345 569 1 ENSG00000146047.7
## 35 25726777 25727345 569 1 ENSG00000146047.7
## 36 25726777 25727345 569 1 ENSG00000146047.7
## 37 25726777 25727345 569 1 ENSG00000146047.7
## 38 25726777 25727345 569 1 ENSG00000146047.7
## 39 25726777 25727345 569 1 ENSG00000146047.7
## 40 25726777 25727345 569 1 ENSG00000146047.7
## 41 25726777 25727345 569 1 ENSG00000146047.7
## 42 25726777 25727345 569 1 ENSG00000146047.7
## 43 25726777 25727345 569 1 ENSG00000146047.7
## 44 25726777 25727345 569 1 ENSG00000146047.7
## 45 25726777 25727345 569 1 ENSG00000146047.7
## 46 25726777 25727345 569 1 ENSG00000146047.7
## 47 25726777 25727345 569 1 ENSG00000146047.7
## 48 26017032 26017787 756 2 ENSG00000124610.5
## 49 26017032 26017787 756 2 ENSG00000124610.5
## 50 26017032 26017787 756 2 ENSG00000124610.5
## 51 26017032 26017787 756 2 ENSG00000124610.5
## 52 26017032 26017787 756 2 ENSG00000124610.5
## 53 26017032 26017787 756 2 ENSG00000124610.5
## 54 26017032 26017787 756 2 ENSG00000124610.5
## 55 26017032 26017787 756 2 ENSG00000124610.5
## 56 26017032 26017787 756 2 ENSG00000124610.5
## 57 26043989 26044357 369 1 ENSG00000234816.2
## 58 26043989 26044357 369 1 ENSG00000234816.2
## 59 26043989 26044357 369 1 ENSG00000234816.2
## 60 26043989 26044357 369 1 ENSG00000234816.2
## 61 26043989 26044357 369 1 ENSG00000234816.2
## 62 26043989 26044357 369 1 ENSG00000234816.2
## 63 26043989 26044357 369 1 ENSG00000234816.2
## 64 26043989 26044357 369 1 ENSG00000234816.2
## 65 26043989 26044357 369 1 ENSG00000234816.2
## 66 26043989 26044357 369 1 ENSG00000234816.2
## 67 26043989 26044357 369 1 ENSG00000234816.2
## 68 26043989 26044357 369 1 ENSG00000234816.2
## 69 26043989 26044357 369 1 ENSG00000234816.2
## 70 26043989 26044357 369 1 ENSG00000234816.2
## 71 26043989 26044357 369 1 ENSG00000234816.2
## 72 26043989 26044357 369 1 ENSG00000234816.2
## 73 26043989 26044357 369 1 ENSG00000234816.2
## 74 26043989 26044357 369 1 ENSG00000234816.2
## 75 26043989 26044357 369 1 ENSG00000234816.2
## 76 26043989 26044357 369 1 ENSG00000234816.2
## 77 26043989 26044357 369 1 ENSG00000234816.2
## 78 26043989 26044357 369 1 ENSG00000234816.2
## 79 26043989 26044357 369 1 ENSG00000234816.2
## 80 26043989 26044357 369 1 ENSG00000234816.2
## 81 26043989 26044357 369 1 ENSG00000234816.2
## 82 26043989 26044357 369 1 ENSG00000234816.2
## 83 26043989 26044357 369 1 ENSG00000234816.2
## 84 26043989 26044357 369 1 ENSG00000234816.2
## 85 26043989 26044357 369 1 ENSG00000234816.2
## 86 26043989 26044357 369 1 ENSG00000234816.2
## 87 68911653 68911759 107 2 ENSG00000206855.1
## 88 78248601 78396894 148294 1 ENSG00000230417.12
## 89 78248601 78396894 148294 1 ENSG00000230417.12
## 90 78248601 78396894 148294 1 ENSG00000230417.12
## 91 78248601 78396894 148294 1 ENSG00000230417.12
## 92 78248601 78396894 148294 1 ENSG00000230417.12
## 93 78267442 78330595 63154 1 ENSG00000230417.12
## 94 78267442 78330595 63154 1 ENSG00000230417.12
## 95 78267442 78330595 63154 1 ENSG00000230417.12
## 96 78301194 78330708 29515 1 ENSG00000230417.12
## 97 78301194 78330708 29515 1 ENSG00000230417.12
## 98 102845595 102845950 356 1 ENSG00000236937.2
## 99 102845595 102845950 356 1 ENSG00000236937.2
## 100 3390780 3391752 973 2 ENSG00000189398.5
## 101 103403512 103404167 656 2 ENSG00000255417.1
## 102 100884702 100884783 82 1 ENSG00000207942.2
## 103 100884702 100884783 82 1 ENSG00000207942.2
## 104 100884702 100884783 82 1 ENSG00000207942.2
## 105 100884702 100884783 82 1 ENSG00000207942.2
## 106 100884702 100884783 82 1 ENSG00000207942.2
## 107 101025564 101025651 88 1 ENSG00000221745.3
## 108 101025564 101025651 88 1 ENSG00000221745.3
## 109 101025564 101025651 88 1 ENSG00000221745.3
## 110 101025564 101025651 88 1 ENSG00000221745.3
## 111 101025564 101025651 88 1 ENSG00000221745.3
## 112 101025564 101025651 88 1 ENSG00000221745.3
## 113 101025564 101025651 88 1 ENSG00000221745.3
## 114 101025564 101025651 88 1 ENSG00000221745.3
## 115 101025732 101025817 86 1 ENSG00000199069.3
## 116 101025732 101025817 86 1 ENSG00000199069.3
## 117 101025732 101025817 86 1 ENSG00000199069.3
## 118 101025732 101025817 86 1 ENSG00000199069.3
## 119 101025732 101025817 86 1 ENSG00000199069.3
## 120 101025732 101025817 86 1 ENSG00000199069.3
## 121 101025732 101025817 86 1 ENSG00000199069.3
## 122 101025732 101025817 86 1 ENSG00000199069.3
## 123 101046455 101046538 84 1 ENSG00000207754.3
## 124 101046455 101046538 84 1 ENSG00000207754.3
## 125 25054210 25054304 95 1 ENSG00000207001.1
## 126 25065026 25065121 96 1 ENSG00000207442.1
## 127 25065026 25065121 96 1 ENSG00000207442.1
## 128 25075929 25076020 92 1 ENSG00000206609.1
## 129 25075929 25076020 92 1 ENSG00000206609.1
## 130 25077051 25077142 92 1 ENSG00000207197.1
## 131 25077051 25077142 92 1 ENSG00000207197.1
## 132 25094037 25094128 92 1 ENSG00000207279.1
## 133 25094037 25094128 92 1 ENSG00000207279.1
## 134 25197576 25197656 81 1 ENSG00000201679.1
## 135 25197576 25197656 81 1 ENSG00000201679.1
## 136 25250859 25250940 82 1 ENSG00000202261.1
## 137 25250859 25250940 82 1 ENSG00000202261.1
## 138 25250859 25250940 82 1 ENSG00000202261.1
## 139 25250859 25250940 82 1 ENSG00000202261.1
## 140 25250859 25250940 82 1 ENSG00000202261.1
## 141 88716278 88716337 60 2 ENSG00000284585.1
## 142 88716278 88716337 60 2 ENSG00000284585.1
## 143 88716278 88716337 60 2 ENSG00000284585.1
## 144 22052430 22091018 38589 1 ENSG00000197134.13
## 145 22052430 22091018 38589 1 ENSG00000197134.13
## 146 22052452 22091103 38652 1 ENSG00000197134.13
## 147 22052452 22091103 38652 1 ENSG00000197134.13
## 148 22052484 22074553 22070 1 ENSG00000197134.13
## 149 22052484 22074553 22070 1 ENSG00000197134.13
## 150 22052484 22091480 38997 1 ENSG00000197134.13
## 151 22052509 22075865 23357 1 ENSG00000197134.13
## 152 22052524 22064332 11809 1 ENSG00000197134.13
## 153 22052536 22088405 35870 1 ENSG00000197134.13
## 154 22052536 22088405 35870 1 ENSG00000197134.13
## 155 22052536 22088405 35870 1 ENSG00000197134.13
## 156 22052536 22088405 35870 1 ENSG00000197134.13
## 157 22052536 22088405 35870 1 ENSG00000197134.13
## 158 22052536 22088405 35870 1 ENSG00000197134.13
## 159 22052536 22088405 35870 1 ENSG00000197134.13
## 160 22052536 22088405 35870 1 ENSG00000197134.13
## 161 22052536 22088405 35870 1 ENSG00000197134.13
## 162 18794529 18796067 1539 1 ENSG00000273148.1
## 163 58818919 58850903 31985 2 ENSG00000235590.7
## 164 58818919 58850903 31985 2 ENSG00000235590.7
## 165 58818919 58850903 31985 2 ENSG00000235590.7
## 166 58818919 58850903 31985 2 ENSG00000235590.7
## 167 58818919 58850903 31985 2 ENSG00000235590.7
## 168 58818919 58850903 31985 2 ENSG00000235590.7
## 169 58818919 58850903 31985 2 ENSG00000235590.7
## 170 58818919 58850903 31985 2 ENSG00000235590.7
## 171 58818919 58850903 31985 2 ENSG00000235590.7
## 172 58818919 58850903 31985 2 ENSG00000235590.7
## 173 58818919 58850903 31985 2 ENSG00000235590.7
## 174 58818919 58850903 31985 2 ENSG00000235590.7
## 175 58818919 58850903 31985 2 ENSG00000235590.7
## 176 58818919 58850903 31985 2 ENSG00000235590.7
## 177 58818919 58850903 31985 2 ENSG00000235590.7
## 178 58818919 58850903 31985 2 ENSG00000235590.7
## 179 58818919 58850903 31985 2 ENSG00000235590.7
## 180 63919756 63919827 72 1 ENSG00000216195.3
## 181 63919756 63919827 72 1 ENSG00000216195.3
## 182 43278125 43279658 1534 2 ENSG00000237206.1
## 183 43278125 43279658 1534 2 ENSG00000237206.1
## 184 4329 4400 72 2 ENSG00000210107.1
## 185 4402 4469 68 1 ENSG00000210112.1
## 186 8527 9207 681 1 ENSG00000198899.2
## 187 8527 9207 681 1 ENSG00000198899.2
## 188 8527 9207 681 1 ENSG00000198899.2
## transcriptId distanceToTSS
## 1 ENST00000514057.1 120
## 2 ENST00000514057.1 195
## 3 ENST00000514057.1 254
## 4 ENST00000514057.1 328
## 5 ENST00000514057.1 332
## 6 ENST00000416634.1 313
## 7 ENST00000417241.1 238
## 8 ENST00000417241.1 252
## 9 ENST00000417241.1 279
## 10 ENST00000447834.1 97
## 11 ENST00000447834.1 33
## 12 ENST00000447834.1 29
## 13 ENST00000447834.1 4
## 14 ENST00000447834.1 -2
## 15 ENST00000501071.2 12
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## 183 ENST00000445028.1 42
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## 186 ENST00000361899.2 195
## 187 ENST00000361899.2 254
## 188 ENST00000361899.2 328BpEval <- ifelse(length(grep('BP', params$TopGO))!=0, TRUE, FALSE)
MfEval <- ifelse(length(grep('MF', params$TopGO))!=0, TRUE, FALSE)
CcEval <- ifelse(length(grep('CC', params$TopGO))!=0, TRUE, FALSE)Therefore:
- universe genes: 36011 genes
- escapee genes: 13396 genes
4.2 TopGO analysis: Biological Process
On the basis of the analysis settings, the enrichment for Biological Process IS performed.
# I generate a list that contains the association between each gene and the GO terms that are associated to it
BPann <- topGO::annFUN.org(whichOnto="BP", feasibleGenes=names(GeneVectors),
mapping="org.Hs.eg.db", ID="symbol") %>% inverseList()
# Wrapper function for topGO analysis
ResBPAll <- topGOResults_new(Genes=GeneVectors, gene2GO=BPann, ontology='BP',
desc=NULL, nodeSize=15, algorithm='weight01', statistic='fisher',
EnTh=params$GoEnTh, PvalTh=params$GoPvalTh, minTerms=12, geneTh=4,
saveRes=TRUE, outDir=paste0(OutputFolder), fileName='BPAll', maxAnn = 500)
## Gene vector contains levels: 0,1
##
## Building most specific GOs .....
## ( 12544 GO terms found. )
##
## Build GO DAG topology ..........
## ( 15945 GO terms and 36197 relations. )
##
## Annotating nodes ...............
## ( 18089 genes annotated to the GO terms. )
##
## -- Weight01 Algorithm --
##
## the algorithm is scoring 5681 nontrivial nodes
## parameters:
## test statistic: fisher
##
## Level 18: 4 nodes to be scored (0 eliminated genes)
##
## Level 17: 8 nodes to be scored (0 eliminated genes)
##
## Level 16: 15 nodes to be scored (60 eliminated genes)
##
## Level 15: 30 nodes to be scored (137 eliminated genes)
##
## Level 14: 69 nodes to be scored (326 eliminated genes)
##
## Level 13: 117 nodes to be scored (695 eliminated genes)
##
## Level 12: 208 nodes to be scored (1891 eliminated genes)
##
## Level 11: 424 nodes to be scored (4277 eliminated genes)
##
## Level 10: 643 nodes to be scored (6618 eliminated genes)
##
## Level 9: 847 nodes to be scored (8803 eliminated genes)
##
## Level 8: 878 nodes to be scored (11449 eliminated genes)
##
## Level 7: 903 nodes to be scored (13612 eliminated genes)
##
## Level 6: 732 nodes to be scored (15707 eliminated genes)
##
## Level 5: 444 nodes to be scored (16765 eliminated genes)
##
## Level 4: 242 nodes to be scored (17432 eliminated genes)
##
## Level 3: 98 nodes to be scored (17697 eliminated genes)
##
## Level 2: 18 nodes to be scored (17834 eliminated genes)
##
## Level 1: 1 nodes to be scored (17896 eliminated genes)Result visualization: Barplot
nterms=20
cols <- c(All='forestgreen', Down='blue', Up='red')
pals <- lapply(cols, {function(el) grDevices::colorRampPalette(c('gold', el))(nterms)})if(nrow(ResBPAll$ResSel)>0){
topGOBarplot_new(TopGORes=ResBPAll$ResSel, terms=nterms, pvalTh=0.01, plotTitle=paste0("All Escapees genes related BP terms"),
palette=pals$All, flip_x=FALSE)
} 
Result visualization: Bubbleplot
if(nrow(ResBPAll$ResSel)>0){
bubbleplot(ResBPAll$ResSel, terms=nterms, Ont = "BP", pvalTh=0.01, plotTitle="All Escapees genes related BP terms")
}
## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
Result visualization: table of genes in top terms
if(nrow(ResBPAll$ResSel)>0){
table_GenesInTerm_BPAll <- TableGenesInTerm(ResBPAll$ResSel, ResBPAll$GOdata, nterms=nterms)
}
table_GenesInTerm_BPAll %>% dplyr::select(-c(Score, GOid)) %>%
datatable(class = 'hover', rownames = FALSE, extension='Buttons', escape = FALSE, caption = paste0("All genes in top ", nterms, " BP terms"), options = list(pageLength=10, dom='Bfrtip', autoWidth=TRUE, buttons=list(c('csv', 'excel'))))4.3 TopGO analysis: Molecular Function
On the basis of the analysis settings, the enrichment for Molecular Function IS performed.
# I generate a list that contains the association between each gene and the GO terms that are associated to it
MFann <- topGO::annFUN.org(whichOnto="MF", feasibleGenes=names(GeneVectors),
mapping="org.Hs.eg.db", ID="symbol") %>% inverseList()
# Wrapper function for topGO analysis
ResMFAll <- topGOResults_new(Genes=GeneVectors, gene2GO=MFann, ontology='MF',
desc=NULL, nodeSize=15, algorithm='weight01', statistic='fisher',
EnTh=params$GoEnTh, PvalTh=params$GoPvalTh, minTerms=12, geneTh=4,
saveRes=TRUE, outDir=paste0(OutputFolder), fileName='MFAll', maxAnn = 500)
## Gene vector contains levels: 0,1
##
## Building most specific GOs .....
## ( 4502 GO terms found. )
##
## Build GO DAG topology ..........
## ( 4948 GO terms and 6418 relations. )
##
## Annotating nodes ...............
## ( 17822 genes annotated to the GO terms. )
##
## -- Weight01 Algorithm --
##
## the algorithm is scoring 1012 nontrivial nodes
## parameters:
## test statistic: fisher
##
## Level 12: 1 nodes to be scored (0 eliminated genes)
##
## Level 11: 11 nodes to be scored (0 eliminated genes)
##
## Level 10: 18 nodes to be scored (17 eliminated genes)
##
## Level 9: 42 nodes to be scored (253 eliminated genes)
##
## Level 8: 75 nodes to be scored (1601 eliminated genes)
##
## Level 7: 151 nodes to be scored (3990 eliminated genes)
##
## Level 6: 200 nodes to be scored (4840 eliminated genes)
##
## Level 5: 233 nodes to be scored (7372 eliminated genes)
##
## Level 4: 199 nodes to be scored (11110 eliminated genes)
##
## Level 3: 64 nodes to be scored (14278 eliminated genes)
##
## Level 2: 17 nodes to be scored (15290 eliminated genes)
##
## Level 1: 1 nodes to be scored (17641 eliminated genes)Result visualization: Barplot
nterms=20
cols <- c(All='forestgreen', Down='blue', Up='red')
pals <- lapply(cols, {function(el) grDevices::colorRampPalette(c('gold', el))(nterms)})if(nrow(ResMFAll$ResSel)>0){
topGOBarplot_new(TopGORes=ResMFAll$ResSel, terms=nterms, pvalTh=0.01, plotTitle=paste0("All Escapees genes related MF terms"),
palette=pals$All, flip_x=FALSE)
} Result visualization: Bubbleplot
if(nrow(ResMFAll$ResSel)>0){
bubbleplot(ResMFAll$ResSel, terms=nterms, Ont = "MF", pvalTh=0.01, plotTitle="All Escapees genes related MF terms")
}Result visualization: table of genes in top terms
if(nrow(ResMFAll$ResSel)>0){
table_GenesInTerm_MFAll <- TableGenesInTerm(ResMFAll$ResSel, ResMFAll$GOdata, nterms=nterms)
table_GenesInTerm_MFAll %>% dplyr::select(-c(Score, GOid)) %>%
datatable(class = 'hover', rownames = FALSE, extension='Buttons', escape = FALSE, caption = paste0("All genes in top ", nterms, " MF terms"), options = list(pageLength=10, dom='Bfrtip', autoWidth=TRUE, buttons=list(c('csv', 'excel'))))
}4.4 TopGO analysis: Cellular Component
On the basis of the analysis settings, the enrichment for Cellular Component IS performed.
# I generate a list that contains the association between each gene and the GO terms that are associated to it
CCann <- topGO::annFUN.org(whichOnto="CC", feasibleGenes=names(GeneVectors),
mapping="org.Hs.eg.db", ID="symbol") %>% inverseList()
# Wrapper function for topGO analysis
ResCCAll <- topGOResults_new(Genes=GeneVectors, gene2GO=CCann, ontology='CC',
desc=NULL, nodeSize=15, algorithm='weight01', statistic='fisher',
EnTh=params$GoEnTh, PvalTh=params$GoPvalTh, minTerms=12, geneTh=4,
saveRes=TRUE, outDir=paste0(OutputFolder), fileName='CCAll', maxAnn = 500)
## Gene vector contains levels: 0,1
##
## Building most specific GOs .....
## ( 1828 GO terms found. )
##
## Build GO DAG topology ..........
## ( 2020 GO terms and 3396 relations. )
##
## Annotating nodes ...............
## ( 18985 genes annotated to the GO terms. )
##
## -- Weight01 Algorithm --
##
## the algorithm is scoring 691 nontrivial nodes
## parameters:
## test statistic: fisher
##
## Level 13: 1 nodes to be scored (0 eliminated genes)
##
## Level 12: 3 nodes to be scored (0 eliminated genes)
##
## Level 11: 34 nodes to be scored (30 eliminated genes)
##
## Level 10: 77 nodes to be scored (87 eliminated genes)
##
## Level 9: 105 nodes to be scored (1180 eliminated genes)
##
## Level 8: 99 nodes to be scored (3407 eliminated genes)
##
## Level 7: 98 nodes to be scored (6147 eliminated genes)
##
## Level 6: 100 nodes to be scored (10364 eliminated genes)
##
## Level 5: 79 nodes to be scored (12750 eliminated genes)
##
## Level 4: 51 nodes to be scored (15455 eliminated genes)
##
## Level 3: 41 nodes to be scored (17751 eliminated genes)
##
## Level 2: 2 nodes to be scored (18616 eliminated genes)
##
## Level 1: 1 nodes to be scored (18870 eliminated genes)Result visualization: Barplot
nterms=20
cols <- c(All='forestgreen', Down='blue', Up='red')
pals <- lapply(cols, {function(el) grDevices::colorRampPalette(c('gold', el))(nterms)})if(nrow(ResCCAll$ResSel)>0){
topGOBarplot_new(TopGORes=ResCCAll$ResSel, terms=nterms, pvalTh=0.01, plotTitle=paste0("All Escapees genes related CC terms"),
palette=pals$All, flip_x=FALSE)
} Result visualization: Bubbleplot
if(nrow(ResCCAll$ResSel)>0){
bubbleplot(ResCCAll$ResSel, terms=nterms, Ont = "CC", pvalTh=0.01, plotTitle="All Escapees genes related CC terms")
}Result visualization: table of genes in top terms
if(nrow(ResCCAll$ResSel)>0){
table_GenesInTerm_CCAll <- TableGenesInTerm(ResCCAll$ResSel, ResCCAll$GOdata, nterms=nterms)
table_GenesInTerm_CCAll %>% dplyr::select(-c(Score, GOid)) %>%
datatable(class = 'hover', rownames = FALSE, extension='Buttons', escape = FALSE, caption = paste0("All genes in top ", nterms, " CC terms"), options = list(pageLength=10, dom='Bfrtip', autoWidth=TRUE, buttons=list(c('csv', 'excel'))))
}5. Saving and Session Info
save.image(paste0(OutputFolder, "AnnotationAndFunctionalEnv.RData"))
saveRDS(AnnotatedEscapees, paste0(OutputFolder, "AnnotatedEscapees.rds"))file_conn <- file(paste0(OutputFolder, "EscapeeGenes_ensembl.txt"), "w")
for (element in gsub(x = EscapeeGenes_ensembl, pattern = "\\..*", replacement = "")) {
cat(element, "\n", file = file_conn)
}
close(file_conn)file_conn <- file(paste0(OutputFolder, "EscapeeGenes_symbol.txt"), "w")
for (element in EscapeeGenes_symbol) {
cat(element, "\n", file = file_conn)
}
close(file_conn)file_conn <- file(paste0(OutputFolder, "GeneUniverse_symbol.txt"), "w")
for (element in GeneUniverse_symbol) {
cat(element, "\n", file = file_conn)
}
close(file_conn)SessionInfo <- sessionInfo()
Date <- date()Date
## [1] "Mon May 5 11:05:31 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] bsseq_1.34.0 SummarizedExperiment_1.28.0
## [3] MatrixGenerics_1.10.0 matrixStats_1.0.0
## [5] GenomicRanges_1.50.2 GenomeInfoDb_1.34.9
## [7] topGO_2.50.0 SparseM_1.81
## [9] GO.db_3.16.0 graph_1.76.0
## [11] viridis_0.6.2 viridisLite_0.4.2
## [13] RColorBrewer_1.1-3 data.table_1.14.8
## [15] DT_0.28 org.Hs.eg.db_3.16.0
## [17] AnnotationDbi_1.60.2 IRanges_2.32.0
## [19] S4Vectors_0.36.2 Biobase_2.58.0
## [21] BiocGenerics_0.44.0 ChIPseeker_1.34.1
## [23] gridExtra_2.3 scales_1.2.1
## [25] dplyr_1.1.2 plotly_4.10.2
## [27] ggplot2_3.4.2
##
## loaded via a namespace (and not attached):
## [1] shadowtext_0.1.2
## [2] fastmatch_1.1-3
## [3] BiocFileCache_2.6.1
## [4] plyr_1.8.8
## [5] igraph_1.5.0
## [6] lazyeval_0.2.2
## [7] splines_4.2.1
## [8] crosstalk_1.2.0
## [9] BiocParallel_1.32.6
## [10] digest_0.6.33
## [11] yulab.utils_0.0.6
## [12] htmltools_0.5.5
## [13] GOSemSim_2.24.0
## [14] fansi_1.0.4
## [15] magrittr_2.0.3
## [16] memoise_2.0.1
## [17] BSgenome_1.66.3
## [18] limma_3.54.2
## [19] Biostrings_2.66.0
## [20] graphlayouts_0.8.4
## [21] R.utils_2.12.2
## [22] enrichplot_1.18.4
## [23] prettyunits_1.1.1
## [24] colorspace_2.1-0
## [25] blob_1.2.4
## [26] rappdirs_0.3.3
## [27] ggrepel_0.9.3
## [28] xfun_0.39
## [29] crayon_1.5.2
## [30] RCurl_1.98-1.12
## [31] jsonlite_1.8.7
## [32] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
## [33] scatterpie_0.1.8
## [34] ape_5.7-1
## [35] glue_1.6.2
## [36] polyclip_1.10-4
## [37] gtable_0.3.3
## [38] zlibbioc_1.44.0
## [39] XVector_0.38.0
## [40] DelayedArray_0.24.0
## [41] Rhdf5lib_1.20.0
## [42] HDF5Array_1.26.0
## [43] DOSE_3.24.2
## [44] DBI_1.1.3
## [45] Rcpp_1.0.11
## [46] plotrix_3.8-2
## [47] progress_1.2.2
## [48] gridGraphics_0.5-1
## [49] tidytree_0.4.2
## [50] bit_4.0.5
## [51] htmlwidgets_1.6.2
## [52] httr_1.4.6
## [53] fgsea_1.24.0
## [54] gplots_3.1.3
## [55] ellipsis_0.3.2
## [56] R.methodsS3_1.8.2
## [57] pkgconfig_2.0.3
## [58] XML_3.99-0.14
## [59] farver_2.1.1
## [60] sass_0.4.7
## [61] dbplyr_2.3.3
## [62] locfit_1.5-9.7
## [63] utf8_1.2.3
## [64] labeling_0.4.2
## [65] ggplotify_0.1.0
## [66] tidyselect_1.2.0
## [67] rlang_1.1.1
## [68] reshape2_1.4.4
## [69] munsell_0.5.0
## [70] tools_4.2.1
## [71] cachem_1.0.8
## [72] cli_3.6.1
## [73] generics_0.1.3
## [74] RSQLite_2.3.1
## [75] evaluate_0.21
## [76] stringr_1.5.0
## [77] fastmap_1.1.1
## [78] yaml_2.3.7
## [79] ggtree_3.6.2
## [80] knitr_1.43
## [81] bit64_4.0.5
## [82] tidygraph_1.2.3
## [83] caTools_1.18.2
## [84] purrr_1.0.1
## [85] KEGGREST_1.38.0
## [86] ggraph_2.1.0
## [87] sparseMatrixStats_1.10.0
## [88] nlme_3.1-162
## [89] R.oo_1.25.0
## [90] aplot_0.1.10
## [91] xml2_1.3.5
## [92] biomaRt_2.54.1
## [93] compiler_4.2.1
## [94] rstudioapi_0.15.0
## [95] filelock_1.0.2
## [96] curl_5.0.1
## [97] png_0.1-8
## [98] treeio_1.23.1
## [99] tibble_3.2.1
## [100] tweenr_2.0.2
## [101] bslib_0.5.0
## [102] stringi_1.7.12
## [103] highr_0.10
## [104] GenomicFeatures_1.50.4
## [105] lattice_0.21-8
## [106] Matrix_1.6-0
## [107] permute_0.9-7
## [108] vctrs_0.6.3
## [109] rhdf5filters_1.10.1
## [110] pillar_1.9.0
## [111] lifecycle_1.0.3
## [112] jquerylib_0.1.4
## [113] cowplot_1.1.1
## [114] bitops_1.0-7
## [115] patchwork_1.1.2
## [116] rtracklayer_1.58.0
## [117] qvalue_2.30.0
## [118] R6_2.5.1
## [119] BiocIO_1.8.0
## [120] KernSmooth_2.23-22
## [121] codetools_0.2-19
## [122] gtools_3.9.4
## [123] boot_1.3-28.1
## [124] MASS_7.3-60
## [125] rhdf5_2.42.1
## [126] rjson_0.2.21
## [127] withr_2.5.0
## [128] GenomicAlignments_1.34.1
## [129] Rsamtools_2.14.0
## [130] GenomeInfoDbData_1.2.9
## [131] parallel_4.2.1
## [132] hms_1.1.3
## [133] grid_4.2.1
## [134] ggfun_0.0.9
## [135] tidyr_1.3.0
## [136] HDO.db_0.99.1
## [137] DelayedMatrixStats_1.20.0
## [138] rmarkdown_2.23
## [139] ggforce_0.4.1
## [140] restfulr_0.0.15