why org.Hs.egGO2ALLEGS contain genes number difference from GO database?
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@yangxiujujuju-21714
Last seen 3.0 years ago
> ls("package:org.Hs.eg.db")
 [1] "org.Hs.eg"                "org.Hs.eg.db"             "org.Hs.eg_dbconn"         "org.Hs.eg_dbfile"        
 [5] "org.Hs.eg_dbInfo"         "org.Hs.eg_dbschema"       "org.Hs.egACCNUM"          "org.Hs.egACCNUM2EG"      
 [9] "org.Hs.egALIAS2EG"        "org.Hs.egCHR"             "org.Hs.egCHRLENGTHS"      "org.Hs.egCHRLOC"         
[13] "org.Hs.egCHRLOCEND"       "org.Hs.egENSEMBL"         "org.Hs.egENSEMBL2EG"      "org.Hs.egENSEMBLPROT"    
[17] "org.Hs.egENSEMBLPROT2EG"  "org.Hs.egENSEMBLTRANS"    "org.Hs.egENSEMBLTRANS2EG" "org.Hs.egENZYME"         
[21] "org.Hs.egENZYME2EG"       "org.Hs.egGENENAME"        "org.Hs.egGO"              "org.Hs.egGO2ALLEGS"      
[25] "org.Hs.egGO2EG"           "org.Hs.egMAP"             "org.Hs.egMAP2EG"          "org.Hs.egMAPCOUNTS"      
[29] "org.Hs.egOMIM"            "org.Hs.egOMIM2EG"         "org.Hs.egORGANISM"        "org.Hs.egPATH"           
[33] "org.Hs.egPATH2EG"         "org.Hs.egPFAM"            "org.Hs.egPMID"            "org.Hs.egPMID2EG"        
[37] "org.Hs.egPROSITE"         "org.Hs.egREFSEQ"          "org.Hs.egREFSEQ2EG"       "org.Hs.egSYMBOL"         
[41] "org.Hs.egSYMBOL2EG"       "org.Hs.egUCSCKG"          "org.Hs.egUNIGENE"         "org.Hs.egUNIGENE2EG"     
[45] "org.Hs.egUNIPROT"

org.Hs.egGO2ALLEGS contain all human terms and genes. But some terms conain genes are less than online GO database. Follow is an example:

> org.Hs.egGO2ALLEGS <- as.list(org.Hs.egGO2ALLEGS)
> org.Hs.egGO2ALLEGS$"GO:0007617"
     ISS      IEA      IEA      ISS      IEA      IEA      IEA      IEA      TAS      IEA      IEA      IEA      IEA      IEA 
   "351"    "551"    "552"   "1812"   "1816"   "2902"   "3066"   "3074"   "4543"   "4808"   "5020"   "5270"   "5728"   "7054" 
     IEA      IEA      IEA      IEA      IEA      IEA      IEA      IEA      IEA 
  "7067"   "7068"   "8648"   "9759"  "23542"  "55585"  "63951"  "84152" "282969" 

ENTREZID convert to SYMBOLID:
> db.term$"GO:0007617"
 [1] "DRD1"     "DRD5"     "MAPK8IP2" "FUOM"     "GRIN1"    "HDAC2"    "HEXB"     "APP"      "MTNR1A"   "NHLH2"    "OXT"     
[12] "SERPINE2" "AVP"      "AVPR1A"   "UBE2Q1"   "PTEN"     "DMRTA1"   "TH"       "THRA"     "THRB"     "PPP1R1B"  "NCOA1"   
[23] "HDAC4"

Follow is "GO:0007617" contain genes which are from online GO database:

DMRTA1  THRB    THRA    PPP1R1B SERPINE2    OXT MAPK8IP2    DRD5    GRIN1
TH  MTNR1A  AVPR1A  kcne2-kcnh2_human       CSDE1   PELO    OR56A5  OR56A4
NCOA1   FUOM    DRD1    HDAC2   HDAC4   AVP NHLH2   APP PTEN
OR56A1  OR5T1   OR13F1  CNOT6   DRD4    DRD3    DRD2    HEXB    UBE2Q1

so ,I want to ask why org.Hs.egGO2ALLEGS' term contain genes less than GO database term? And where can I get tems of contain genes complete?

org.Hs.eg.db org.Hs.egGO2ALLEGS • 756 views
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@martin-morgan-1513
Last seen 13 hours ago
United States

Please provide the output of sessionInfo() or at least

> packageVersion("org.Hs.eg.db")
[1] '3.8.2'

Note the source of the GO annotations in the package

> org.Hs.eg.db
OrgDb object:
| DBSCHEMAVERSION: 2.1
| Db type: OrgDb
...
| GOSOURCENAME: Gene Ontology
| GOSOURCEURL: ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest-lite/
| GOSOURCEDATE: 2019-Apr24
| GOEGSOURCEDATE: 2019-Apr26
| GOEGSOURCENAME: Entrez Gene
| GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
...

From the NCBI, I am lead to here (click on the Organism button and the + sign beside Homo sapiens) where I see 23 human genes associated with GO:0007617. This is how many I see in the org pacakge

> unique(select(org.Hs.eg.db, "GO:0007617", "SYMBOL", "GOALL")[,'SYMBOL'])
'select()' returned 1:many mapping between keys and columns
 [1] "APP"      "AVP"      "AVPR1A"   "DRD1"     "DRD5"     "GRIN1"
 [7] "HDAC2"    "HEXB"     "MTNR1A"   "NHLH2"    "OXT"      "SERPINE2"
[13] "PTEN"     "TH"       "THRA"     "THRB"     "NCOA1"    "HDAC4"
[19] "MAPK8IP2" "UBE2Q1"   "DMRTA1"   "PPP1R1B"  "FUOM"

What source would you like to use?

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Hello Martin! Thanks for your answer! I fill confused´╝îyesterday I serch GO:0007617 on the gene ontology (Organism button and the + sign beside Homo sapiens), the result is 35 genes[ https://ibb.co/XyyTW4K]. This is just an example, some others org terms also has less genes than gene ontology(such as GO:0060255).

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What is the URL that you are using to capture the image? For me I am using the URL http://amigo.geneontology.org/amigo/search/bioentity?q=*:*&fq=regulates_closure:%22GO:0007617%22

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My URL is the same as you. http://amigo.geneontology.org/amigo/search/bioentity?q=:&fq=regulates_closure:%22GO:0007617%22. The image was cut out by me Two day ago. Now I serch GO:0007617 on the gene ontology (Organism button and the + sign beside Homo sapiens), the result is 23 genes which is the same as org package.

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yes, I also find genes in org.Bt.egGO2ALLEGS (bovine) are always less than online GO database in the same term. So do you know how to get the gene list that have annotations from online GO database? Thanks

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@yangxiujujuju-21714
Last seen 3.0 years ago

Hello Martin! Thanks for your answer! I fill confused´╝îyesterday I serch GO:0007617 on the gene ontology (Organism button and the + sign beside Homo sapiens), the result is 35 genes[https://ibb.co/XyyTW4K]. This is just an example, some others org terms also has less genes than gene ontology(such as GO:0060255).

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