人与小鼠基因名称互相转换

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在R中，如需对人和小鼠的基因名进行互相转换，可以使用biomaRt程序包。

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> library(biomaRt)
> human <- useMart("ensembl",dataset="hsapiens_gene_ensembl")
> mouse <- useMart("ensembl",dataset="mmusculus_gene_ensembl")
# 可以查看Attributes
> head(listAttributes(mouse),100)[,1]
  [1] "ensembl_gene_id"                 "ensembl_gene_id_version"        
  [3] "ensembl_transcript_id"           "ensembl_transcript_id_version"  
  [5] "ensembl_peptide_id"              "ensembl_peptide_id_version"     
  [7] "ensembl_exon_id"                 "description"                    
  [9] "chromosome_name"                 "start_position"                 
 [11] "end_position"                    "strand"                         
 [13] "band"                            "transcript_start"               
 [15] "transcript_end"                  "transcription_start_site"       
 [17] "transcript_length"               "transcript_tsl"                 
 [19] "transcript_gencode_basic"        "transcript_appris"              
 [21] "external_gene_name"              "external_gene_source"           
 [23] "external_transcript_name"        "external_transcript_source_name"
 [25] "transcript_count"                "percentage_gene_gc_content"     
 [27] "gene_biotype"                    "transcript_biotype"             
 [29] "source"                          "transcript_source"              
 [31] "version"                         "transcript_version"             
 [33] "peptide_version"                 "external_synonym"               
 [35] "phenotype_description"           "source_name"                    
 [37] "study_external_id"               "strain_name"                    
 [39] "strain_gender"                   "p_value"                        
 [41] "go_id"                           "name_1006"                      
 [43] "definition_1006"                 "go_linkage_type"                
 [45] "namespace_1003"                  "goslim_goa_accession"           
 [47] "goslim_goa_description"          "ccds"                           
 [49] "chembl"                          "clone_based_ensembl_gene"       
 [51] "clone_based_ensembl_transcript"  "entrezgene_trans_name"          
 [53] "embl"                            "arrayexpress"                   
 [55] "genedb"                          "ottg"                           
 [57] "ottt"                            "ottp"                           
 [59] "hgnc_id"                         "hgnc_symbol"                    
 [61] "protein_id"                      "kegg_enzyme"                    
 [63] "merops"                          "mgi_description"                
 [65] "mgi_symbol"                      "mgi_id"                         
 [67] "mgi_trans_name"                  "mirbase_accession"              
 [69] "mirbase_id"                      "entrezgene_description"         
 [71] "entrezgene_accession"            "entrezgene_id"                  
 [73] "pdb"                             "reactome"                       
 [75] "reactome_gene"                   "refseq_mrna"                    
 [77] "refseq_mrna_predicted"           "refseq_ncrna"                   
 [79] "refseq_ncrna_predicted"          "refseq_peptide"                 
 [81] "refseq_peptide_predicted"        "rfam"                           
 [83] "rnacentral"                      "hgnc_trans_name"                
 [85] "ucsc"                            "uniparc"                        
 [87] "uniprot_gn_symbol"               "uniprot_gn_id"                  
 [89] "uniprotswissprot"                "uniprotsptrembl"                
 [91] "vega_gene"                       "vega_transcript"                
 [93] "vega_translation"                "wikigene_description"           
 [95] "wikigene_name"                   "wikigene_id"                    
 [97] "affy_mg_u74a"                    "affy_mg_u74av2"                 
 [99] "affy_mg_u74b"                    "affy_mg_u74bv2"      
# 基因名称对应的Attributes在小鼠中是"mgi_symbol"，在人中是"hgnc_symbol"
> geneHs = c("TP53","TSC1")
# 上面是人的三个基因名称，如需转换成小鼠基因，使用如下语法：
> geneMm <- getLDS(attributes = "hgnc_symbol",filters="hgnc_symbol",values=geneHs,mart=human,attributesL = "mgi_symbol",martL=mouse,uniqueRows = TRUE)
> geneMm
  HGNC.symbol MGI.symbol
1        TSC1       Tsc1
2        TP53      Trp53
# 同理，如需将小鼠基因转成人的基因，不举例子
> geneHs <- getLDS(attributes = "mgi_symbol",filters="mgi_symbol",values=genes,mart=mouse,attributesL = "hgnc_symbol",martL=human,uniqueRows = TRUE)
  • 本文作者：括囊无誉
  • 本文链接： R/gene-symbol-trans/
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