[BioC] Discrepancies finding genes with a given GO term

[Oscar Rueda]

Dear list, 

I'm trying to find the list of genes with a given go term. I'm using two
different methods and I get different results for amigo web page.
If I use: 

> library(GO.db)
> library(org.Hs.eg.db)
> res <- get("GO:0006913", revmap(org.Hs.egGO))
> res <- do.call('c', mget(res, org.Hs.egSYMBOL))
> sort(unique(res))
 [1] "AAAS"    "ANKRD54" "ANP32A"  "CAMK1"   "CDK5"    "EIF5A"   "MLX"
 [8] "MLXIP"   "MYBBP1A" "NPM1"    "NUP155"  "NUP205"  "NUP98"   "RAN"
[15] "RBM15B"  "RSRC1"   "SET"     "ZNF384"
 

I get 18 genes. According to amigo, AXIN1, CAMK4, NUP62, UPF3A and UPF3B
should be there too.

If I use biomaRt I get:

> library(biomaRt)
> ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> res <- getBM(c("hgnc_symbol"), filters = "go", values = "GO:0006913", mart =
ensembl)
> sort(unique(res[,1]))
  [1] "AAAS"    "ANKRD54" "ANP32A"  "AXIN1"   "CAMK1"   "CAMK4"   "CDC42"
  [8] "CDK5"    "DIRAS1"  "DIRAS2"  "DIRAS3"  "DNAJC27" "EFCAB4B" "EIF5A"
 [15] "HRAS"    "IFT27"   "KRAS"    "LRRK2"   "MLX"     "MLXIP"   "MRAS"
 [22] "MYBBP1A" "NPM1"    "NRAS"    "NUP155"  "NUP205"  "NUP54"   "NUP98"
 [29] "NUPL1"   "RAB10"   "RAB11A"  "RAB11B"  "RAB12"   "RAB13"   "RAB14"
 [36] "RAB15"   "RAB17"   "RAB18"   "RAB19"   "RAB1A"   "RAB1B"   "RAB20"
 [43] "RAB21"   "RAB22A"  "RAB23"   "RAB24"   "RAB25"   "RAB26"   "RAB27A"
 [50] "RAB27B"  "RAB28"   "RAB2A"   "RAB2B"   "RAB30"   "RAB31"   "RAB32"
 [57] "RAB33A"  "RAB33B"  "RAB34"   "RAB35"   "RAB36"   "RAB37"   "RAB38"
 [64] "RAB39"   "RAB39B"  "RAB3A"   "RAB3B"   "RAB3C"   "RAB3D"   "RAB40A"
 [71] "RAB40AL" "RAB40B"  "RAB40C"  "RAB41"   "RAB42P1" "RAB43"   "RAB43P1"
 [78] "RAB44"   "RAB4A"   "RAB4B"   "RAB5A"   "RAB5B"   "RAB5C"   "RAB6A"
 [85] "RAB6B"   "RAB6C"   "RAB7A"   "RAB7L1"  "RAB8A"   "RAB8B"   "RAB9A"
 [92] "RAB9B"   "RABL2A"  "RABL2B"  "RAC1"    "RAC2"    "RAC3"    "RALA"
 [99] "RALB"    "RAN"     "RAP1A"   "RAP1B"   "RAP2A"   "RAP2B"   "RAP2C"
[106] "RASD1"   "RASD2"   "RASEF"   "RASL11B" "RASL12"  "REM1"    "REM2"
[113] "RERG"    "RHOA"    "RHOB"    "RHOC"    "RHOD"    "RHOF"    "RHOG"
[120] "RHOH"    "RHOJ"    "RHOQ"    "RHOU"    "RHOV"    "RIT1"    "RIT2"
[127] "RND2"    "RND3"    "RRAS"    "RRAS2"   "RSRC1"   "SET"     "ZNF384"

This is a bigger list.

I don't know exactly what's happening here. Can anyone tell me what am I
doing wrong?

Cheers, 
Oscar

> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] biomaRt_2.6.0        org.Hs.eg.db_2.4.6   GO.db_2.4.5
[4] RSQLite_0.9-2        DBI_0.2-5            AnnotationDbi_1.12.0
[7] Biobase_2.10.0

loaded via a namespace (and not attached):
[1] RCurl_1.4-3  tools_2.12.0 XML_3.2-0



Oscar M. Rueda, PhD.
Postdoctoral Research Fellow, Breast Cancer Functional Genomics.
Cancer Research UK Cambridge Research Institute.
Li Ka Shing Centre, Robinson Way.
Cambridge CB2 0RE 
England 




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