I am trying to retrieve full gene lists for a given GO id (like
"GO:0060973"), limiting to human genes. The R code I am using is
shown below. When run, just two genes are returned, but the AmiGO2
page for that pathway
https://amigo.geneontology.org/amigo/term/GO:0060973
returns 20 or so genes.
I think this is because my query is only returning genes with a "GO
class (direct)" exactly matching the queried pathway ("cell migration
involved in heart development"), but I would like to also include the genes from
sub-pathways shown on the AmiGO2 page (like "cell migration involved
in coronary vasculogenesis").
I know I must be able to specify this in the filters somehow, but I
have been searching for quite a while and just can't figure it out.
> library(org.Hs.eg.db)
> select(org.Hs.eg.db, "GO:0060973", "SYMBOL", "GOALL")
'select()' returned 1:many mapping between keys and columns
GOALL EVIDENCEALL ONTOLOGYALL SYMBOL
1 GO:0060973 IEA BP BMP4
2 GO:0060973 IEA BP BMP7
3 GO:0060973 IEA BP CDC42
4 GO:0060973 IEA BP EDN1
5 GO:0060973 IEA BP EDNRA
6 GO:0060973 IEA BP ENG
7 GO:0060973 ISS BP FOLR1
8 GO:0060973 ISS BP NOTCH1
9 GO:0060973 ISS BP PDGFRB
10 GO:0060973 ISS BP PITX2
11 GO:0060973 ISS BP SNAI2
12 GO:0060973 TAS BP TBX5
13 GO:0060973 IEA BP TWIST1
14 GO:0060973 IMP BP DCHS1
15 GO:0060973 IEA BP HAND2
16 GO:0060973 ISS BP SEMA3C
17 GO:0060973 IEA BP BVES
18 GO:0060973 ISS BP FLRT3
19 GO:0060973 ISS BP MESP1
20 GO:0060973 IEA BP NDRG4
21 GO:0060973 IDA BP MIR1-1