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Question: org.Hs.eg "gene_info" table seems to be worng
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gravatar for Vladimir Morozov
8.0 years ago by
Vladimir Morozov130 wrote:
Hi, org.Hs.eg "gene_info" table seems to be worng > conn <- org.Hs.eg_dbconn() #the example seems correct > dbGetQuery(conn, "SELECT * FROM gene_info LIMIT 3;") _id gene_name symbol 1 1 alpha-1-B glycoprotein A1BG 2 2 alpha-2-macroglobulin A2M 3 3 alpha-2-macroglobulin pseudogene A2MP #wrong for other genes... > dbGetQuery(conn, "SELECT * FROM gene_info where _id=367 or _id=11835;") dbGetQuery(conn, "SELECT * FROM gene_info where _id=367 or _id=11835;") _id gene_name symbol 1 367 ADP-ribosyltransferase 1 ART1 2 11835 phosphoserine aminotransferase 1 PSAT1 > "111835" is mouse AR gene Individual maps look Ok > org.Hs.egSYMBOL[["367"]] [1] "AR" > org.Hs.egSYMBOL[["11835"]] NULL > org.Hs.egGENENAME[["367"]] [1] "androgen receptor" > > org.Hs.eg() org.Hs.eg() Quality control information for org.Hs.eg: This package has the following mappings: org.Hs.egACCNUM has 29687 mapped keys (of 40784 keys) org.Hs.egACCNUM2EG has 590454 mapped keys (of 590454 keys) org.Hs.egALIAS2EG has 102986 mapped keys (of 102986 keys) org.Hs.egCHR has 40539 mapped keys (of 40784 keys) org.Hs.egCHRLENGTHS has 25 mapped keys (of 25 keys) org.Hs.egCHRLOC has 20599 mapped keys (of 40784 keys) org.Hs.egCHRLOCEND has 20599 mapped keys (of 40784 keys) org.Hs.egENSEMBL has 20255 mapped keys (of 40784 keys) org.Hs.egENSEMBL2EG has 19903 mapped keys (of 19903 keys) org.Hs.egENSEMBLPROT has 19927 mapped keys (of 40784 keys) org.Hs.egENSEMBLPROT2EG has 44871 mapped keys (of 44871 keys) org.Hs.egENSEMBLTRANS has 19965 mapped keys (of 40784 keys) org.Hs.egENSEMBLTRANS2EG has 44931 mapped keys (of 44931 keys) org.Hs.egENZYME has 2015 mapped keys (of 40784 keys) org.Hs.egENZYME2EG has 870 mapped keys (of 870 keys) org.Hs.egGENENAME has 40784 mapped keys (of 40784 keys) org.Hs.egGO has 17482 mapped keys (of 40784 keys) org.Hs.egGO2ALLEGS has 10438 mapped keys (of 10438 keys) org.Hs.egGO2EG has 7659 mapped keys (of 7659 keys) org.Hs.egMAP has 36549 mapped keys (of 40784 keys) org.Hs.egMAP2EG has 2946 mapped keys (of 2946 keys) org.Hs.egOMIM has 14080 mapped keys (of 40784 keys) org.Hs.egOMIM2EG has 16415 mapped keys (of 16415 keys) org.Hs.egPATH has 4799 mapped keys (of 40784 keys) org.Hs.egPATH2EG has 205 mapped keys (of 205 keys) org.Hs.egPFAM has 24009 mapped keys (of 40784 keys) org.Hs.egPMID has 28206 mapped keys (of 40784 keys) org.Hs.egPMID2EG has 232955 mapped keys (of 232955 keys) org.Hs.egPROSITE has 24009 mapped keys (of 40784 keys) org.Hs.egREFSEQ has 28158 mapped keys (of 40784 keys) org.Hs.egREFSEQ2EG has 90796 mapped keys (of 90796 keys) org.Hs.egSYMBOL has 40784 mapped keys (of 40784 keys) org.Hs.egSYMBOL2EG has 40763 mapped keys (of 40763 keys) org.Hs.egUNIGENE has 24864 mapped keys (of 40784 keys) org.Hs.egUNIGENE2EG has 25562 mapped keys (of 25562 keys) org.Hs.egUNIPROT has 20652 mapped keys (of 40784 keys) Additional Information about this package: DB schema: HUMAN_DB DB schema version: 1.0 Organism: Homo sapiens Date for NCBI data: 2009-Mar11 Date for GO data: 200903 Date for KEGG data: 2009-Mar10 Date for Golden Path data: 2008-Sep3 Date for IPI data: 2009-Mar03 Date for Ensembl data: 2009-Mar6 ********************************************************************** ***************** The information contained in this electronic message is ...{{dropped:18}}
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ADD COMMENTlink modified 8.0 years ago by Marc Carlson7.2k • written 8.0 years ago by Vladimir Morozov130
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gravatar for Marc Carlson
8.0 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Vladimir, The _id value in the gene_info table is NOT meant to be an entrez gene ID. It is an internal ID ONLY. If a few genes have the same _id as their entrez gene ID, that is only a bizarre coincidence and has no actual meaning whatsoever. In order to connect the values in the gene_info table to an actual entrez gene ID, you need to join the gene_info table to the genes table by using the internal _id. That is what _id is for, just an integer for joining the various internal tables to each other. The schema for this packages is available by using org.Hs.eg_dbschema(). And it might be also be a good idea to read the AnnotationDbi vignette which can be found here: http://www.bioconductor.org/packages/release/bioc/html/AnnotationDbi.h tml Let me know if you have more questions, Marc Vladimir Morozov wrote: > Hi, > > org.Hs.eg "gene_info" table seems to be worng > > > >> conn <- org.Hs.eg_dbconn() >> > > #the example seems correct > >> dbGetQuery(conn, "SELECT * FROM gene_info LIMIT 3;") >> > _id gene_name symbol > 1 1 alpha-1-B glycoprotein A1BG > 2 2 alpha-2-macroglobulin A2M > 3 3 alpha-2-macroglobulin pseudogene A2MP > > #wrong for other genes... > >> dbGetQuery(conn, "SELECT * FROM gene_info where _id=367 or _id=11835;") >> > > dbGetQuery(conn, "SELECT * FROM gene_info where _id=367 or _id=11835;") > _id gene_name symbol > 1 367 ADP-ribosyltransferase 1 ART1 > 2 11835 phosphoserine aminotransferase 1 PSAT1 > > > > > "111835" is mouse AR gene > > Individual maps look Ok > >> org.Hs.egSYMBOL[["367"]] >> > [1] "AR" > > >> org.Hs.egSYMBOL[["11835"]] >> > NULL > > >> org.Hs.egGENENAME[["367"]] >> > [1] "androgen receptor" > > > > >> org.Hs.eg() >> > > org.Hs.eg() > Quality control information for org.Hs.eg: > > > This package has the following mappings: > > org.Hs.egACCNUM has 29687 mapped keys (of 40784 keys) > org.Hs.egACCNUM2EG has 590454 mapped keys (of 590454 keys) > org.Hs.egALIAS2EG has 102986 mapped keys (of 102986 keys) > org.Hs.egCHR has 40539 mapped keys (of 40784 keys) > org.Hs.egCHRLENGTHS has 25 mapped keys (of 25 keys) > org.Hs.egCHRLOC has 20599 mapped keys (of 40784 keys) > org.Hs.egCHRLOCEND has 20599 mapped keys (of 40784 keys) > org.Hs.egENSEMBL has 20255 mapped keys (of 40784 keys) > org.Hs.egENSEMBL2EG has 19903 mapped keys (of 19903 keys) > org.Hs.egENSEMBLPROT has 19927 mapped keys (of 40784 keys) > org.Hs.egENSEMBLPROT2EG has 44871 mapped keys (of 44871 keys) > org.Hs.egENSEMBLTRANS has 19965 mapped keys (of 40784 keys) > org.Hs.egENSEMBLTRANS2EG has 44931 mapped keys (of 44931 keys) > org.Hs.egENZYME has 2015 mapped keys (of 40784 keys) > org.Hs.egENZYME2EG has 870 mapped keys (of 870 keys) > org.Hs.egGENENAME has 40784 mapped keys (of 40784 keys) > org.Hs.egGO has 17482 mapped keys (of 40784 keys) > org.Hs.egGO2ALLEGS has 10438 mapped keys (of 10438 keys) > org.Hs.egGO2EG has 7659 mapped keys (of 7659 keys) > org.Hs.egMAP has 36549 mapped keys (of 40784 keys) > org.Hs.egMAP2EG has 2946 mapped keys (of 2946 keys) > org.Hs.egOMIM has 14080 mapped keys (of 40784 keys) > org.Hs.egOMIM2EG has 16415 mapped keys (of 16415 keys) > org.Hs.egPATH has 4799 mapped keys (of 40784 keys) > org.Hs.egPATH2EG has 205 mapped keys (of 205 keys) > org.Hs.egPFAM has 24009 mapped keys (of 40784 keys) > org.Hs.egPMID has 28206 mapped keys (of 40784 keys) > org.Hs.egPMID2EG has 232955 mapped keys (of 232955 keys) > org.Hs.egPROSITE has 24009 mapped keys (of 40784 keys) > org.Hs.egREFSEQ has 28158 mapped keys (of 40784 keys) > org.Hs.egREFSEQ2EG has 90796 mapped keys (of 90796 keys) > org.Hs.egSYMBOL has 40784 mapped keys (of 40784 keys) > org.Hs.egSYMBOL2EG has 40763 mapped keys (of 40763 keys) > org.Hs.egUNIGENE has 24864 mapped keys (of 40784 keys) > org.Hs.egUNIGENE2EG has 25562 mapped keys (of 25562 keys) > org.Hs.egUNIPROT has 20652 mapped keys (of 40784 keys) > > > Additional Information about this package: > > DB schema: HUMAN_DB > DB schema version: 1.0 > Organism: Homo sapiens > Date for NCBI data: 2009-Mar11 > Date for GO data: 200903 > Date for KEGG data: 2009-Mar10 > Date for Golden Path data: 2008-Sep3 > Date for IPI data: 2009-Mar03 > Date for Ensembl data: 2009-Mar6 > > > > ******************************************************************** ******************* > The information contained in this electronic message is ...{{dropped:18}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD COMMENTlink written 8.0 years ago by Marc Carlson7.2k
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