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  • 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:

    library(ggplot2)
    library(RColorBrewer)
    
    Hdac1.chipseq.1 <- read.csv("ChIPseq/Hdac1_targets_mm_ESC_CR.txt", sep = "	", 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

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  • 原文地址:https://www.cnblogs.com/leezx/p/14603559.html
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