RcisTarget is an R-package to identify transcription factor (TF) binding motifs over-represented on a gene list.
基于转录因子靶基因的 TSS 位点上下游，是否具有该转录因子结合的 motif 富集，将靶基因区分为直接靶基因和间接靶基因，从而保留直接靶基因。
安装
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
# To support paralell execution:
BiocManager::install(c("doMC", "doRNG"))
# For the examples in the follow-up section of the tutorial:
BiocManager::install(c("DT", "visNetwork"))
BiocManager::install(RcisTarget)
workflow
输入：Gene list and motif databases( which should be chosen depending on the organism and the search space around the TSS of the genes)
library(RcisTarget)
# Load gene sets to analyze. e.g.:
geneList1 <- read.table(file.path(system.file('examples', package='RcisTarget'), "hypoxiaGeneSet.txt"), stringsAsFactors=FALSE)[,1]
geneLists <- list(geneListName=geneList1) # 构建为列表
# Select motif database to use (i.e. organism and distance around TSS)
data(motifAnnotations_hgnc)
motifRankings <- importRankings("~/databases/hg19-tss-centered-10kb-7species.mc9nr.feather")
# Motif enrichment analysis:
motifEnrichmentTable_wGenes <- cisTarget(geneLists, motifRankings,
motifAnnot=motifAnnotations_hgnc)
需要的数据库
- Gene-motif rankings: which provides the rankings (~score) of all the genes for each motif.
- The annotation of motifs to transcription factors.
