非模式物种GO/KEGG富集分析

前言:
微博参与话题 #给你四年时间你也学不会生信#

先前的富集分析教程^[1]主要是以模式物种人为例子，展开的分析，今天在B站看了孟浩巍视频教程^[2]，学习新的技能，豁然开朗，欣然记之。

本文主要针对非模式物种，但是有参考基因组可用

1. R包安装及database下载

# non-model, but have the genome
> source("https://bioconductor.org/biocLite.R")
> biocLite("AnnotationHub") 
> biocLite("biomaRt") 
# load package
> library(AnnotationHub)
> library(biomaRt)
# make a orgDb
> hub <- AnnotationHub::AnnotationHub()
这里以桔小实蝇为例
# fruit fly = bactrocera dorsalis
> query(hub, "bactrocera")

搜索后结果如下：

> query(hub, "bactrocera")
AnnotationHub with 9 records
# snapshotDate(): 2018-04-30 
# $dataprovider: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/
# $species: Bactrocera (Bactrocera)_dorsalis, Bactrocera (Bactrocera)_latifrons, Bactrocera (Dacul...
# $rdataclass: OrgDb
# additional mcols(): taxonomyid, genome, description, coordinate_1_based, maintainer,
#   rdatadateadded, preparerclass, tags, rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH62538"]]' 
            title                                           
  AH62538 | org.Bactrocera_(Bactrocera)_latifrons.eg.sqlite 
  AH62539 | org.Bactrocera_latifrons.eg.sqlite              
  AH62542 | org.Bactrocera_(Daculus)_oleae.eg.sqlite        
  AH62543 | org.Bactrocera_(Dacus)_oleae.eg.sqlite          
  AH62544 | org.Bactrocera_oleae.eg.sqlite                  
  AH62568 | org.Bactrocera_(Zeugodacus)_cucurbitae.eg.sqlite
  AH62569 | org.Bactrocera_cucurbitae.eg.sqlite             
  AH62581 | org.Bactrocera_(Bactrocera)_dorsalis.eg.sqlite  
  AH62582 | org.Bactrocera_dorsalis.eg.sqlite 

我们选择AH62582 | org.Bactrocera_dorsalis.eg.sqlite并下载它

> Bactrocera.OrgDb <- hub[["AH62582"]]

如果报错，可能是缺少依赖的安装包，可以按照提示依次下载，两种方法

1. install.packages("packages")
2. source("https://bioconductor.org/biocLite.R")
   biocLite("pacakges")

2. 查看注释信息

> columns(Bactrocera.OrgDb)
 [1] "ACCNUM"      "ALIAS"       "CHR"         "ENTREZID"    "EVIDENCE"    "EVIDENCEALL" "GENENAME"   
 [8] "GID"         "GO"          "GOALL"       "ONTOLOGY"    "ONTOLOGYALL" "PMID"        "REFSEQ"     
[15] "SYMBOL" 
> Bactrocera.OrgDb
OrgDb object:
| DBSCHEMAVERSION: 2.1
| DBSCHEMA: NOSCHEMA_DB
| ORGANISM: Bactrocera dorsalis
| SPECIES: Bactrocera dorsalis
| CENTRALID: GID
| Taxonomy ID: 27457
| Db type: OrgDb
| Supporting package: AnnotationDbi
Please see: help('select') for usage information
# 查看注释信息的每一列
> head(keys(Bactrocera.OrgDb,keytype = "ALIAS")）
[1] "AAA62341.1" "AAA62342.1" "AAA62343.1" "AAA62344.1" "AAF22478.1" "AAL17758.1"
实际上，ALIAS内包含了“omitted 17518 entries”

3. GO富集分析

# 对BP(Biological process)进行富集分析
# 只需将OrgDb数据库替换为我们下载好的非模式物种库即可。
> enrich.go.BP = enrichGO(gene       = DEG.gene_symbol,
                        OrgDb        = Bactrocera.OrgDb,
                        keyType      = 'ENTREZID',ont= "BP",
                        pvalueCutoff = 0.01,
                        qvalueCutoff = 0.05,
                        readable     = T)
> barplot(enrich.go.BP)
> dotplot(enrich.go.BP)

p_value: 富集显著性，统计显著性要去小于0.01；
q_value: 对p_value的修正，在多次统计检验时，需要有修正值；
q_value一定大于p_value

4. KEGG富集分析

# 只需将OrgDb数据库替换为我们下载好的非模式物种库即可。
> enrichKEGG(gene        =  DEG.gene_symbol,
          OrgDb          = Bactrocera.OrgDb,
          keyType        = 'ENTREZID',
          ont            = "DO",
          pvalueCutoff   = 0.01,
          qvalueCutofF   = 0.05,
          readable       = T)

5. GO出图解读

纵轴为GO中每一term，例如Legionellosis；
横轴为GeneRatio，即输入的基因，term在整体基因中所占的百分数；
圆圈大小表示count的数目；
p.adjust：p越小，圆越大，结果越可靠；

Rplot22.png

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1. 利用clusterProfiler进行富集分析 ↩

2. 生物信息学教程-GO, KEGG, DO富集分析 ↩