简单的基因ID转换

基因ID转换有很多方法,对高手如饮水吃饭,对新手来说却是很难逾越的高山,我推荐两个简单迅速的方法:

一 网页工具

https://biodbnet-abcc.ncifcrf.gov/db/db2db.php
哪里不会点哪里

二 R语言org.Hs.eg.db 系列包

suppressMessages(library(org.Hs.eg.db))# 载入包
keytypes(org.Hs.eg.db) #查看支持对选项
####方式一
[1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS" "ENTREZID"     "ENZYME"      
[8] "EVIDENCE"     "EVIDENCEALL"  "GENENAME"     "GO"           "GOALL"        "IPI"          "MAP"         
[15] "OMIM"         "ONTOLOGY"     "ONTOLOGYALL"  "PATH"         "PFAM"         "PMID"         "PROSITE"     
[22] "REFSEQ"       "SYMBOL"       "UCSCKG"       "UNIGENE"      "UNIPROT"    
gene_list<-select(org.Hs.eg.db, keys=as.character(your genes), columns=c("SYMBOL","ENTREZID"), keytype="ENSEMBL") #keytype是你输入基因编号类型,columns是你输出对基因编号类型,基因怎么导入不再赘述。
gene_list[1:4,1:3]
         ENSEMBL  SYMBOL ENTREZID
1 ENSG00000125352 RNF113A     7737
2 ENSG00000048162   NOP16    51491
3 ENSG00000205542  TMSB4X     7114
4 ENSG00000205542  TMSB4X     7114
结果是一个矩阵,想怎么提取就怎么提取。

#####方式二
entrezIDs <- mget(genenames, org.Hs.egSYMBOL2EG, ifnotfound=NA)

方式三

Y叔的包

library(clusterProfiler)
data(geneList, package="DOSE")
gene <- names(geneList)[abs(geneList) > 2]
gene.df <- bitr(gene, fromType = "ENTREZID",
        toType = c("ENSEMBL", "SYMBOL"),
        OrgDb = org.Hs.eg.db)
head(gene.df)

方法四

biomaRt

suppressMessages(library(biomaRt))
#chr should be number only
#from the chr to gene name
mart <- useEnsembl(biomart='ensembl', 
                   dataset="hsapiens_gene_ensembl") 
check_filters_rt<-listFilters(mart)
check_out_rt<-listAttributes(mart)
results <- getBM(attributes = c("hgnc_symbol", "chromosome_name", "start_position", "end_position","gene_biotype"), 
                 filters = c("chromosome_name", "start", "end"), 
                 values = list(human_df_sig_pick[,"chr"], human_df_sig_pick[,"start"], human_df_sig_pick[,"end"]), mart = mart)
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