Find genes that are associated with a known gene ontology term:
#install if you don't have org.Hs.eg.db and GO.db
source("http://bioconductor.org/biocLite.R")
biocLite("org.Hs.eg.db")
biocLite("GO.db")
library(org.Hs.eg.db)
library(GO.db)
go_id = GOID( GOTERM[ Term(GOTERM) == "chromatin remodeling"])
get(go_id, org.Hs.egGO2ALLEGS)
IEA IEA IDA IEA IEA IDA TAS IC
"86" "473" "664" "676" "1105" "2186" "2648" "3065"
IC ISS IEA ISS TAS IDA IEA TAS
"3066" "3070" "4221" "4678" "5925" "5928" "6594" "6595"
IDA IEA IDA IDA IMP TAS NAS NAS
"6597" "6598" "6599" "6601" "6602" "6827" "6829" "6830"
IEA IDA TAS IEA TAS IEA NAS IEA
"6927" "7141" "7141" "7270" "8289" "8467" "8850" "9031"
IDA NAS IDA TAS IDA TAS IEA NAS
"9557" "9757" "9759" "10014" "10361" "10629" "10661" "11176"
NAS IMP IEA IDA IMP NAS IDA NAS
"11335" "22893" "23314" "23411" "50511" "50943" "51773" "54108"
IDA TAS IMP NAS IMP IDA NAS IEA
"54617" "55193" "55355" "57492" "57680" "79723" "84181" "150572"
IMP NAS
"201161" "373861"
allegs = get(go_id, org.Hs.egGO2ALLEGS)
genes = unlist(mget(allegs,org.Hs.egSYMBOL))
genes
86 473 664 676 1105 2186 2648 3065
"ACTL6A" "RERE" "BNIP3" "BRDT" "CHD1" "BPTF" "KAT2A" "HDAC1"
3066 3070 4221 4678 5925 5928 6594 6595
"HDAC2" "HELLS" "MEN1" "NASP" "RB1" "RBBP4" "SMARCA1" "SMARCA2"
6597 6598 6599 6601 6602 6827 6829 6830
"SMARCA4" "SMARCB1" "SMARCC1" "SMARCC2" "SMARCD1" "SUPT4H1" "SUPT5H" "SUPT6H"
6927 7141 7141 7270 8289 8467 8850 9031
"HNF1A" "TNP1" "TNP1" "TTF1" "ARID1A" "SMARCA5" "KAT2B" "BAZ1B"
9557 9757 9759 10014 10361 10629 10661 11176
"CHD1L" "MLL4" "HDAC4" "HDAC5" "NPM2" "TAF6L" "KLF1" "BAZ2A"
11335 22893 23314 23411 50511 50943 51773 54108
"CBX3" "BAHD1" "SATB2" "SIRT1" "SYCP3" "FOXP3" "RSF1" "CHRAC1"
54617 55193 55355 57492 57680 79723 84181 150572
"INO80" "PBRM1" "HJURP" "ARID1B" "CHD8" "SUV39H2" "CHD6" "SMYD1"
201161 373861
"CENPV" "HILS1"
See also: org.Hs.eg.db
Source: bioconductor mailing list thread -> [BioC] Query Gene Ontology
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Attribution 4.0 International License.
Hi? thanks for you giving this example about extract gene names according to GO terms!
Can I ask you a question about how to extract GO terms? Do you konw that? Waiting for your answer, thank you very much!
Hi, what do you mean extracting GO terms? Can you give me an example of what you want to do?
Hi!
Thank you very much for this example!
It seems that it retrieves only the first gene of each GOID are am I misunderstanding something?
If it is the case, how can one get all the genes of each GO term?
Thanks,
Best,
Pernille