Cistrome数据库挖掘转录因子靶基因 | TF | target

进入http://cistrome.org/db/#/数据库

 

输入你感兴趣的转录因子，比如HDAC1

 

选择物种，以及你感兴趣的cell type

 

点击可以查询”check a putative target“

 

也可以下载全部的”Putative Target“

 

最后个性化绘图

 

总结：

适合辅助分析，提供额外的fancy的证据，还是有一定的power的。

 

绘图代码：

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library(ggplot2) library(RColorBrewer)   Hdac1.chipseq.1 <- read.csv("ChIPseq/Hdac1_targets_mm_ESC_CR.txt", sep = "\t", stringsAsFactors = F) Hdac1.chipseq.1$humanGene <- toupper(Hdac1.chipseq.1$symbol) Hdac1.chipseq.1$cellLine <- "mm_ESC_CR" Hdac1.chipseq.1$CellType <- "Embryonic Stem Cell"   Hdac1.chipseq <- rbind(Hdac1.chipseq.1, Hdac1.chipseq.2, Hdac1.chipseq.3, Hdac1.chipseq.4, Hdac1.chipseq.5) dim(Hdac1.chipseq)   # sort score Hdac1.chipseq <- Hdac1.chipseq[order(Hdac1.chipseq$score, decreasing = T),]   # remove duplicates Hdac1.chipseq <- Hdac1.chipseq[!duplicated(Hdac1.chipseq[,c("chrom","symbol","cellLine")]),]   core.risk.genes <- c("GLI3","BCL11A","FOXO1","HEY1","HEY2","SOX11","ASCL1","TUBB3","TFAP2A","NR2F2")   Hdac1.chipseq.core <- subset(Hdac1.chipseq, humanGene %in% core.risk.genes & score > 0)   Hdac1.chipseq.core$humanGene <- factor(Hdac1.chipseq.core$humanGene, levels = unique(Hdac1.chipseq.core$humanGene)) Hdac1.chipseq.core$CellType <- factor(Hdac1.chipseq.core$CellType, levels = c("iPSC", "Embryonic Stem Cell", "Embryonic Fibroblast Cell", "Epithelium"))   options(repr.plot.width=7, repr.plot.height=5) p <- ggplot(Hdac1.chipseq.core, aes(x=humanGene, y=score, color=CellType)) +   # facet_wrap(~variable, ncol = 3) +   theme_bw() +   # geom_violin(trim=T, scale="width") + # aes(fill=group) # width, area, count   # geom_boxplot() +   geom_jitter(position=position_jitter(0),aes(fill=CellType),shape = 21,colour = "grey50",size = 4,stroke = 1) +   labs(title="HDAC1",x="", y = "Score from ChIP-seq") +   # theme(legend.title=element_blank()) +   # just remove inside grid   theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) +   # remove top and right border   theme(axis.line = element_line(colour = "black"), panel.grid.major = element_blank(),     panel.grid.minor = element_blank(), panel.border = element_blank(), panel.background = element_blank()) +   # force y start from 0   # scale_y_continuous(expand = c(0, 0), limits = c(-0.3, 11.5)) +   # title position   theme(plot.title = element_text(hjust = 0.5, face = "italic", size=20)) +   ##   theme(# legend.position = "none",         axis.text.x = element_text(angle = 60, size = 12, vjust = 0.5, face = "italic"),         axis.title.y = element_text(size = 16)) +   scale_color_manual(values=brewer.pal(8,"Set1")) +   scale_fill_manual(values=brewer.pal(8,"Set1")) p   ggsave(filename = "../manuscript/HDAC1.target.score.pdf", width = 7, height = 5)

　　

成品图

看着还不错吧，可以扯上一扯。

 

参考目录：human/singleCell/HSCR/HDAC/HDAC.ipynb