R与DAVID注释的区别2020-01-04

library(ggplot2)
library(clusterProfiler)
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")

library(org.Hs.eg.db)
df <- bitr(unique(DEG$symbol), fromType = "SYMBOL",
toType = c( "ENTREZID"),
OrgDb = org.Hs.eg.db)
head(df)
DEG=DEG[rownames(DEG)%in%gene,]

head(DEG)

DEG=merge(DEG,df,by.y='SYMBOL',by.x='symbol')
head(DEG)
save(DEG,file = 'anno_DEG_SM.Rdata')

gene_up= DEG[DEGg == 'DOWN','ENTREZID']
gene_diff=c(gene_up,gene_down)
gene_all=as.character(DEG[ ,'ENTREZID'] )
data(geneList, package="DOSE")
head(geneList)
boxplot(geneList)
boxplot(DEG$logFC)

geneList=DEGENTREZID
geneList=sort(geneList,decreasing = T)

以上是geneList 的做取，共得到659个差异基因与其ENTREZID

head(geneList)
3952 6781 1356 29923 8516 6581
6.729912 6.439553 5.081165 5.007642 4.877560 4.814260

接下来对基因进行KEGG分析

kk.diff <- enrichKEGG(gene = gene_diff,
organism = 'hsa',
pvalueCutoff = 0.05)
head(kk.diff)[,1:6]

head(kk.diff)[,1:6]
[1] ID Description GeneRatio BgRatio
[5] pvalue p.adjust
<0 行> (或0-长度的row.names)

当P值选取0.05的时候没有有价值的结果。

kk.diff <- enrichKEGG(gene = gene_diff,

•                     organism     = 'hsa',
  

•                     pvalueCutoff = 0.99)
  

head(kk.diff)[,1:6]
ID Description
hsa04514 hsa04514 Cell adhesion molecules (CAMs)
hsa04151 hsa04151 PI3K-Akt signaling pathway
hsa04510 hsa04510 Focal adhesion
hsa05418 hsa05418 Fluid shear stress and atherosclerosis
hsa04015 hsa04015 Rap1 signaling pathway
GeneRatio BgRatio pvalue p.adjust
hsa04514 12/237 147/7946 0.001431242 0.1867090
hsa04151 21/237 354/7946 0.001988208 0.1867090
hsa04510 14/237 199/7946 0.002454145 0.1867090
hsa05418 11/237 139/7946 0.002861440 0.1867090
hsa04015 14/237 210/7946 0.004001455 0.2088759
barplot(kk.diff,showCategory = 20,title="Pathway enrichment")

当P值选为0.99是出来的结果也较少，且矫正P值颇高。 kegg_jianshu.png

GO注释的话情况类似。

接下来用同样的一批基因去网页在线注释。

DAVID和KOBAS得出的结果前5个和R包做的结果基本一致，但是网上注释的结果明显更多。 简述.png 简述图.png

用R做的结果显示的是矫正P值，数值基本都大于0.05。
且通路太少，仅有五个，我已经将P值的最低阈值设定为0.99了还是很少。

以上R与DAVID、KOBAS的注释对比，我觉得KOBAS的结果更好一些，但是绘图什么的可能不如R方便。