has been employed to analyze genome-wide ROIs, such as open chromatin regions obtained by DNase-seq32 and ATAC-seq.33 To facilitate biological interpretation of genome-wide regions, we implemented a function, seq2gene, in ChIPseeker to associate genomic regions with coding genes through many-to-many mapping. It automatically maps genomic regions to host genes (either located in exon or intron), proximal genes (located in the promoter region), and flanking genes (located upstream and downstream within user-specified distance). The seq2gene function supports a wide variety of species if a genomic annotation, such as the TxDb (UCSC-based) or EnsDb (Ensembl-based) object, is available. After mapping genomic regions to coding genes, clusterProfiler can be employed to perform functional enrichment analysis of the coding genes to assign biological meanings to the set of genomic regions. The combination of ChIPseeker and clusterProfiler allows more biological ontology or pathway databases to be utilized to explore functions of genomic regions for a wide variety of species.library(ChIPseeker)## the file can be downloaded using ‘downloadGSMbedFiles("GSM1295076")’file <- "GSM1295076_CBX6_BF_ChipSeq_mergedReps_peaks.bed.gz"gr <- readPeakFile(file)library(TxDb.Hsapiens.UCSC.hg19.knownGene)TxDb <- TxDb.Hsapiens.UCSC.hg19.knownGenegenes <- seq2gene(gr, tssRegion=c(-1000, 1000), flankDistance = 3000, TxDb)library(clusterProfiler)g <- bitr(genes, ‘ENTREZID’, ‘SYMBOL’, ‘org.Hs.eg.db’)## downloaded fromhttps://maayanlab.cloud/Enrichr/geneSetLibrary?mode=text&libraryName=ENCODE_and_ChEA_Consensus_TFs_from_ChIP-Xencode <- read.gmt("ENCODE_and_ChEA_Consensus_TFs_from_ChIP-X.txt")enricher(g$SYMBOL, TERM2GENE=encode)
