Obtaining Go Term Probabilities

Question

[Venky]

Hey All,

I need to get convert the following:

xxx2233 GO:0000166      ubc8 (ubiquitin conjugating enzyme 8) protein binding ubiquitin-protein ligase
xxx2234 GO:0005525      nrpb6a dna binding dna-directed rna polymerase
xxx2235 GO:0007264      nrpb6a dna binding dna-directed rna polymerase

to the following:

xxx2233 0.564738        GO:0000166      ubc8 (ubiquitin conjugating enzyme 8) protein binding ubiquitin-protein ligase
xxx2234 0.456987        GO:0005525      nrpb6a dna binding dna-directed rna polymerase
xxx2235 0.192837        GO:0007264      nrpb6a dna binding dna-directed rna polymerase

Essentially, i need to obtain the probability of occurrence of a GO term for every gene in the result

Is anyone aware of any script or a tool to obtain these probabilities provided the input file mentioned above?

Thanks,

[Sean Davis]

It isn't clear what "probability" you want to find. Can you supply an example or at least give us the numbers you would use to calculate your result?

[Jason]

I'm also a little unclear as to what you want. Do you just want the percentage of genes that have each GO term you specify or maybe the percentages for all GO terms? Also, what species are you working with?

Answer 1

[NetunoPoncã]

If you are talking about a list of GO terms, can't you use a tool like GO Stat?

http://gostat.wehi.edu.au/cgi-bin/goStat.pl