go kegg

非模式生物进行GO/KEGG富集分析

非模式生物富集分析存在着缺少注释等问题，而clusterProfiler不仅针对模式生物，对非模式生物也能进行富集，并且支持用户自定义注释文件，可以说是相当友好了。

R包及依赖下载安装

source("https://bioconductor.org/biocLite.R")

biocLite("AnnotationHub")

biocLite("biomaRt")

biocLite("clusterProfiler")

# load package

library(AnnotationHub)

library(biomaRt)

library(clusterProfiler)

clusterProfiler主要通过OrgDb进行富集分析，Bioconductor自带20个OrgDb可供使用，多半是模式生物，可以通过AnnotationHub在线检索并抓取OrgDb。以嗜热四膜虫(Tetrahymena thermophila)为例。

hub AnnotationHub()

query(hub, "Tetrahymena thermophila")

AnnotationHub with 2 records

# snapshotDate(): 2017-10-27

# $dataprovider: Inparanoid8, ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/

# $species: Tetrahymena thermophila, Tetrahymena thermophila SB210

# $rdataclass: Inparanoid8Db, OrgDb

# additional mcols(): taxonomyid, genome, description,

# coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,

# rdatapath, sourceurl, sourcetype

# retrieve records with, e.g., 'object[["AH10445"]]'

title

AH10445 | hom.Tetrahymena_thermophila.inp8.sqlite

AH59150 | org.Tetrahymena_thermophila_SB210.eg.sqlite

选择带有注释信息的org数据

annoDB hub[["AH59150"]]

注释

可以对注释信息进行查看

> annoDB

OrgDb object:

| DBSCHEMAVERSION: 2.1

| DBSCHEMA: NOSCHEMA_DB

| ORGANISM: Tetrahymena thermophila_SB210

| SPECIES: Tetrahymena thermophila_SB210

| CENTRALID: GID

| Taxonomy ID: 312017

| Db type: OrgDb

| Supporting package: AnnotationDbi

Please see: help('select') for usage information

> columns(annoDB)

[1] "ACCNUM" "ALIAS" "ENTREZID" "EVIDENCE" "EVIDENCEALL"

[6] "GENENAME" "GID" "GO" "GOALL" "ONTOLOGY"

[11] "ONTOLOGYALL" "PMID" "REFSEQ" "SYMBOL"

#查看注释信息每一列

> head(keys(annoDB,keytype = "ALIAS"))

[1] "NEWENTRY" "TTHERM_000000023" "TTHERM_000000031" "TTHERM_000000042"

[5] "TTHERM_000000045" "TTHERM_000000090"

GO富集分析

#挑选100个ENTREZ基因ID进行富集，也可以使用bitr来转换ID，甚至于直接检索GO注释

#newID

> sample_genes keys(annoDB)[1:100]

> head(sample_genes)

[1] "7822955" "7822974" "7823109" "7823219" "7823307" "7823613"

go enrichGO(sample_genes, OrgDb=annoDB, pvalueCutoff=0.05, qvalueCutoff=0.2, readable = T)

> barplot(go)

> dotplot(go)

KEGG富集分析

kegg enrichKEGG(sample_genes,keyType = 'kegg',organism = 'tet',pvalueCutoff = 0.01,qvalueCutoff = 0.05)

#可以使用bitr_kegg功能转换ID

ke bitr_kegg(sample_genes, fromType='Path', toType='ncbi-proteinid', organism='tet')

#不过fromType或者toType只支持'kegg' 'ncbi-geneid' 'ncbi-proteinid'或者'uniprot'

search_kegg_organism('ece', by='kegg_code')

可以从https://www.genome.jp/kegg/catalog/org_list.html查找支持KEGG分析的物种的list