[BioC] bioMart GO inconsistency, normal?
rtt at wayne.edu
Fri Aug 9 01:30:29 CEST 2013
I am a graduate student at Wayne State University in Detroit. I am running BioMart to collect GO terms for lists of genes and I noticed that some genes are annotated with top nodes (eg "biological_process") and others are not. I wonder if any one can tell me why.
An example code and my sessionInfo are below. In this example, I collect all human HUGO gene symbols using the HGNChelper package. From those, I use BioMart to get the GO terms for these genes, and take only the "biological_process" (BP) annotations.
There are 15368 unique genes that have BP annotations (uniqGenesInGO).
Then , I split the list of all BP annotations into those which include "GO:0008150" (which is the "biological_process" term), and those which do not.
596 genes are annotated with "GO:0008150", and 14772 are not. This is inconsistent!
Thanks for your help,
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
data(hgnc.table) # gives names of all approved symbols
allHgnc <- unique(hgnc.table[,2])
allGOhgnc <- getBM(attributes = c("go_id", "go_linkage_type", "entrezgene","hgnc_symbol","namespace_1003"), filters = "hgnc_symbol", values = allHgnc, mart = ensembl)
# load("allGOhgnc.RData") 266749
BP <- allGOhgnc[which(allGOhgnc$namespace_1003 == "biological_process"),] # 126789 human BP terms in GO
BP<-BP[!duplicated(BP),] # 108019
uniqGenesInGO <- unique(BP$hgnc_symbol) # 15368
# "GO:0008150" is "biological_process"
hasBPtab <- BP[which(BP$go_id == "GO:0008150"), ]
length(hasBP) # 596
noBPtab<-BP[ -which(BP$hgnc_symbol %in% hasBP), ]
length(unique(noBPtab$hgnc_symbol)) # 14772
# 14772 + 596 = 15368
# why are some genes annotated with the top node and others are not??
R version 3.0.0 (2013-04-03)
Platform: x86_64-unknown-linux-gnu (64-bit)
 LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
 LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
 LC_PAPER=C LC_NAME=C
 LC_ADDRESS=C LC_TELEPHONE=C
 LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
loaded via a namespace (and not attached):
 RCurl_1.95-4.1 XML_3.96-1.1
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