Trouble using biomaRt to pull pathway genes from GO
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cstorer • 0
@e1a78c66
Last seen 11 months ago
United States

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("biomaRt")

ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")

gene.data <- getBM(attributes=c('hgnc_symbol', 
'ensembl_transcript_id', 'go_id'), filters = 'go', values = 
'GO:0060973',mart=ensembl)

unique(gene.data$hgnc_symbol)

[1] "BVES"  "NDRG4"
GO biomaRt • 698 views
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@james-w-macdonald-5106
Last seen 2 hours ago
United States

Using biomaRt:

> mart <- useEnsembl("ensembl","hsapiens_gene_ensembl")
> getBM(c("ensembl_gene_id","hgnc_symbol", "go_id"), "go_parent_term", "GO:0060973", mart)
   ensembl_gene_id hgnc_symbol      go_id
1  ENSG00000101144        BMP7 GO:1905312
2  ENSG00000125378        BMP4 GO:1905312
3  ENSG00000078401        EDN1 GO:0003253
4  ENSG00000122691      TWIST1 GO:0003253
5  ENSG00000112276        BVES GO:0060973
6  ENSG00000019549       SNAI2 GO:0003273
7  ENSG00000075223      SEMA3C GO:1905312
8  ENSG00000151617       EDNRA GO:0003253
9  ENSG00000164107       HAND2 GO:0003253
10 ENSG00000113721      PDGFRB GO:0060981
11 ENSG00000148400      NOTCH1 GO:0003273
12 ENSG00000125848       FLRT3 GO:0003345
13 ENSG00000089225        TBX5 GO:0060980
14 ENSG00000110195       FOLR1 GO:0003147
15 ENSG00000110195       FOLR1 GO:0003253
16 ENSG00000166823       MESP1 GO:0003259
17 ENSG00000166823       MESP1 GO:0003260
18 ENSG00000166823       MESP1 GO:0060975
19 ENSG00000166341       DCHS1 GO:0003273
20 ENSG00000164093       PITX2 GO:0003253
21 ENSG00000103034       NDRG4 GO:0060973
22 ENSG00000106991         ENG GO:0003273
23 ENSG00000070831       CDC42 GO:0003253

Or a much faster way

> 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
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