RNASEQ分析入门笔记10-clusterProfiler富集分析

一、安装clusterProfiler

source(“https://bioconductor.org/biocLite.R") # 如果报错，请尝试http://
biocLite(“clusterProfiler”)
library(clusterProfiler) # 载入包，测试是否安装成功，如果提示找不到某个包，则安装相关的包即可，比如我的电脑提示“不存在叫‘rvcheck’这个名字的程辑包”，则使用如下语法安装“rvcheck”，如缺乏其他包，也是同理。
install.packages(“rvcheck”)

二、安装基因组注释数据

目前，Bioconductor官网支持19种生物的注释数据，可以直接安装：

biocLite(“org.Hs.eg.db”) # 安装人类的注释数据
library(org.Hs.eg.db) # 测试，载入人类的注释数据
biocLite(“org.Mm.eg.db”) # 安装小鼠的注释数据
library(org.Mm.eg.db) # 测试，载入小鼠的注释数据

三、载入基因列表

data <- read.csv("top50.csv") # 从文件中载入数据，并赋值给data
# 我们需要的是第二列的基因列表，因此，只筛选第二列即可
gene <- data[,2] # 抽取第二列，赋值给gene
gene <- bitr(gene,fromType="SYMBOL",toType="ENTREZID",OrgDb=org.Hs.eg.db) # groupGO默认使用"ENTREZID"作为输入数据，因此首先将“SYMBOL”转化为“ENTREZID”，以防出错
gene <- gene[,2] # 抽取第二列作为input

四、groupGO分析

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ggo <- groupGO(gene=gene,OrgDb=org.Hs.eg.db,ont="BP",level=3,readable=TRUE)
ggo <- groupGO(gene=gene,OrgDb=org.Hs.eg.db,ont="CC",level=3,readable=TRUE)
ggo <- groupGO(gene=gene,OrgDb=org.Hs.eg.db,ont="MF",level=3,readable=TRUE)

groupGO命令的格式为：groupGO(gene,OrgDb,ont,level,readable)

gene，指定前景基因文件，即要分析的基因集合，默认为”ENTREZID”格式；
OrgDb，指定基因组注释数据；
ont，即ontology，参数有三个，分别为CC，BP和MF，对应：细胞组分（cellular component，CC），生物过程（biological process，BP），分子功能（molecular function，MF）；
level，指定分析的GO水平；
readable，逻辑值，TRUE或FALSE；

1	head(as.data.frame(ggo)) # 查看前六行，结果是六行五列的数据

ID Description Count
GO:0019953 GO:0019953 sexual reproduction 7
GO:0019954 GO:0019954 asexual reproduction 0
GO:0022414 GO:0022414 reproductive process 26
GO:0032504 GO:0032504 multicellular organism reproduction 9
GO:0032505 GO:0032505 reproduction of a single-celled organism 0
GO:0061887 GO:0061887 reproduction of symbiont in host 0
GeneRatio
GO:0019953 7/298
GO:0019954 0/298
GO:0022414 26/298
GO:0032504 9/298
GO:0032505 0/298
GO:0061887 0/298
geneID
GO:0019953 APOB/ABAT/ANG/AR/AVPR1A/LEPR/ACOX1
GO:0019954
GO:0022414 APOB/AGT/AMBP/RBP4/ABAT/SERPINF1/ANG/HNF4A/AR/AVPR1A/ARG1/LEPR/GJB1/BOK/DHODH/SLC38A3/PDGFRA/TBX3/ADGRG1/IGFBP2/TTPA/ACOX1/DBH/ETNK2/NAMPT/HSD17B2
GO:0032504 APOB/SERPINF1/ANG/AR/AVPR1A/ARG1/PDGFRA/ACOX1/DBH
GO:0032505
GO:0061887

五、groupGo结果可视化

1	barplot(ggo,drop=TRUE,showCategory=20)

ggo barplot.jpeg

六、enrichGO分析

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ego <- enrichGO(gene=gene,universe=names(geneList),OrgDb=org.Hs.eg.db,ont="BP",pvalueCutoff=0.01,qvalueCutoff=0.05,readable=TRUE)
ego <- enrichGO(gene=gene,universe=names(geneList),OrgDb=org.Hs.eg.db,ont="CC",pvalueCutoff=0.01,qvalueCutoff=0.05,readable=TRUE)
ego <- enrichGO(gene=gene,universe=names(geneList),OrgDb=org.Hs.eg.db,ont="MF",pvalueCutoff=0.01,qvalueCutoff=0.05,readable=TRUE)

enrichGO命令语法：enrichGO(gene,universe,OrgDb,ont,pvalueCutoff,qvalueCutoff,readable)

universe，背景基因文件，可以使用默认值；

1	head(as.data.frame(ego))

ID Description
GO:0072562 GO:0072562 blood microparticle
GO:0042627 GO:0042627 chylomicron
GO:0031093 GO:0031093 platelet alpha granule lumen
GO:0005788 GO:0005788 endoplasmic reticulum lumen
GO:0034361 GO:0034361 very-low-density lipoprotein particle
GO:0034385 GO:0034385 triglyceride-rich plasma lipoprotein particle
GeneRatio BgRatio pvalue p.adjust qvalue
GO:0072562 33/288 101/11817 9.367691e-29 2.519909e-26 2.336992e-26
GO:0042627 8/288 11/11817 1.750866e-11 2.354915e-09 2.183975e-09
GO:0031093 14/288 62/11817 1.938754e-10 1.738416e-08 1.612227e-08
GO:0005788 26/288 247/11817 3.097572e-10 2.083117e-08 1.931907e-08
GO:0034361 8/288 16/11817 1.227828e-09 5.504763e-08 5.105180e-08
GO:0034385 8/288 16/11817 1.227828e-09 5.504763e-08 5.105180e-08
geneID
GO:0072562 ITIH4/ALB/FGB/FGA/FGG/ORM1/HPX/HP/VTN/APOA2/AGT/AMBP/SERPINC1/F2/C3/C9/SERPING1/HRG/ITIH1/SERPINA3/AHSG/GC/APOA4/PLG/KNG1/TF/C4BPA/C8G/C8A/APOA1/HPR/ITIH2/C1S
GO:0042627 APOB/APOC3/APOA2/APOA4/APOH/APOA1/LSR/APOC1
GO:0031093 ALB/FGB/FGA/FGG/ORM1/SERPINA1/SERPING1/HRG/SERPINA3/AHSG/F5/PLG/KNG1/VWF
GO:0005788 APOB/ALB/FGA/FGG/SERPINA1/VTN/APOA2/SERPINC1/F2/C3/IGFBP1/AHSG/F5/SERPIND1/APOA4/KNG1/TF/PROC/APOA1/F9/ITIH2/MTTP/F10/CES2/H6PD/CDH2
GO:0034361 APOB/APOC3/APOA2/APOA4/APOH/APOA1/LSR/APOC1
GO:0034385 APOB/APOC3/APOA2/APOA4/APOH/APOA1/LSR/APOC1
Count
GO:0072562 33
GO:0042627 8
GO:0031093 14
GO:0005788 26
GO:0034361 8
GO:0034385 8