利用KEGG数据库进行ID转换

利用KEGG数据库进行ID转换clusterProfilercanconvertbiologicalIDsusingOrgDbobjectviathebitrfunction.NowIimplementedanotherfunction,bitr_keggforconvertingIDsthroughKEGGAPI.library(clusterProfiler)data(gcSample)hghead(hg)##[1]'4597''7111''5266''2175''755''23046'eg2np##Warninginbitr_kegg(hg,fromType='kegg',toType='ncbi-proteinid',##organism='hsa'):3.7%ofinputgeneIDsarefailtomap...head(eg2np)##keggncbi-proteinid##18326NP_003499##258487NP_001034707##3139081NP_619647##459272NP_068576##5993NP_001780##62676NP001487np2uphead(np2up)##ncbi-proteiniduniprot##1 NP_005457 O75586##2 NP_005792 P41567##3 NP_005792 Q6IAV3##4 NP_037536 Q13421##5 NP_006054 O60662##6 NP_001092002 O95398TheIDtype(bothfromType&toType)shouldbeoneof'kegg','ncbi-geneid','ncbi-proteinid'or'uniprot'.The'kegg'istheprimaryIDusedinKEGGdatabase.ThedatasourceofKEGGwasfromNCBI.Aruleofthumbforthe'kegg'IDisentrezgeneIDforeukaryotespeciesandLocusIDforprokaryotes.Manyprokaryotespeciesdon'thaveentrezgeneIDavailable.Forexamplewecancheckthegeneinformationofece:Z5100inhttp://www.genome.jp/dbget-bin/www_bget?ece:Z5100,whichhaveNCBI-ProteinIDandUnitProtlinksintheOtherDBsEntry,butnotNCBI-GeneID.IfwetrytoconvertZ5100toncbi-geneid,bitr_keggwillthrowerrorofncbi-geneidisnotsupported.bitr_kegg('Z5100',fromType='kegg',toType='ncbi-geneid',organism='ece')##ErrorinKEGG_convert(fromType,toType,organism):##ncbi-geneidisnotsupportedforece...Wecanofcourseconvertittoncbi-proteinidanduniprot:bitr_kegg('Z5100',fromType='kegg',toType='ncbi-proteinid',organism='ece')##keggncbi-proteinid##1Z5100 AAG58814bitr_kegg('Z5100',fromType='kegg',toType='uniprot',organism='ece')##kegguniprot##1Z5100Q7DB85search_kegg_organismclusterProfilersupportsmorethan4kspecieslistedinhttp://www.genome.jp/kegg/catalog/org_list.htmlforhypergeometrictest(enrichKEGG&enrichMKEGG)andGSEA(gseKEGG&gseMKEGG).Wecanusebitr_keggtoconvertIDforallthese4kspecies.Tofacilitatesearchingscientificnameabbreviateusedintheorganismparameterofthesefunctions,Iimplementedthesearch_kegg_organismfunction.Wecansearchbykegg_code,scientific_nameorcommon_name(whichisnotavailableforprokaryotes).search_kegg_organism('ece',by='kegg_code')##kegg_code

scientific_namecommon_name##334eceEscherichiacoliO157:H7EDL933(EHEC)ecolidim(ecoli)##[1]643head(ecoli)##kegg_codehead(ecoli)##kegg_codescientificnamecommonname##329ecoEscherichiacoliK-12##329ecoEscherichiacoliK-12MG1655##330ecjEscherichiacoliK-12##330ecjEscherichiacoliK-12W3110##331ecdEscherichiacoliK-12##331ecdEscherichiacoliK-12DH10B##332ebwEscherichiacoli##332ebwEscherichiacoliBW2952##333ecokEscherichiacoliK-12##333ecokEscherichiacoliK-12MDS42##334eceEscherichiacoliO157:H7EDL933##334(EHEC)keyTypeparameterWiththeIDconversionutilitiesbuiltinclusterProfiler,IaddaparameterkeyTypeinenrichKEGG,enrichMKEGG,gseKEGGandgseMKEGG.Nowwecan

useIDtypethatisnottheprimaryIDinKEGGdatabase.xhead(summary(x))## IDDescriptionGeneRatio##hsa04072hsa04072PhospholipaseDsignalingpathway11/133##hsa04060hsa04060Cytokine-cytokinereceptorinteraction14/133##hsa04390hsa04390pathway10/133##hsa04975hsa04975absorption5/133interaction14/133##hsa04390hsa04390pathway10/133##hsa04975hsa04975absorption5/133##hsa05221hsa05221leukemia 6/133## BgRatioqvalueHipposignalingFatdigestionandAcutemyeloidpvaluep.adjust##hsa04072216/92750.00026541900.039016590.03240905##hsa04060354/92750.00053492450.039316950.03265855##hsa04390213/92750.00095362470.041994040.03488227##hsa0497558/92750.00140148860.04199404

0.03488227##hsa0522186/92750.00142836870.041994040.03488227##genelD##hsa04072O95398/Q99777/P49619/Q6FGP0/Q8WVM9/O14807/P41594/A8K5P7/P10145/A0A024RDA5/P16234##hsa04060A0N0N3/O00574/P19876/P01589/P10145/A0A024RDA5/B4DGA4/Q99665/P16234/P78556/Q6I9S7/P42830/P27930/Q9UBN6##hsa04390Q8WW10/A8K141/Q9UI47/P35240/A0A024R1J8/Q659G9/Q9UJU2/P22003/M9VUD0/O00144##hsa04975Q9UNK4/A0A087WZT4/A0A0C4DFX6/Q9UHC9/P04054##hsa05221Q659G9/Q9UJU2/Q03181/A0A024RCW6/Q06455/B2R6I9## Count##hsa0407211

##hsa0407211##hsa0406014##hsa04390##hsa0406014##hsa0439010##hsa04975##hsa05221setReadableForGOanalysis,wehaveareadableparametertocontrolwhethertraslatingtheIDstohumanreadablegenename.ThisparameterisnotavailableforKEGGanalysis.ButwestillhavetheabilitytotranslateinputgeneIDstogenenameusingsetReadablefunctionifandonlyifcorrespondingOrgDbobjectisavailable.yhead(summary(y))##IDhead(summary(y))##IDDescriptionGeneRatio##hsa04072hsa04072PhospholipaseDsignaling##hsa04072hsa04072PhospholipaseDsignalingpathway11/133##hsa04060hsa04060Cytokine-cytokinereceptorinteraction14/133##hsa04390hsa04390Hipposignaling##hsa04390hsa04390Hipposignalingpathway10/133##hsa04975hsa04975Fatdigestionand##hsa04975hsa04975Fatdigestionandabsorption5/133##hsa05221hsa05221Acutemyeloidleukemia6/133##hsa05221hsa05221Acutemyeloidleukemia6/133##BgRatiopvaluep.adjust##BgRatiopvaluep.adjustqvalue##hsa04072216/92750.00026541900.039016590.03240905##hsa04060354/92750.00053492450.039316950.03265855##hsa04390213/92750.00095362470.041994040.03488227##hsa0497558/92750.00140148860.041994040.03488227##hsa0522186/92750.00142836870.041994040.03488227##geneID##hsa04072RAPGEF3/RAPGEF3/DGKG/MRAS/MRAS/MRAS/GRM5/GRM5/C