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[go-friends] Is there a standard format for GO term enrichment results?

Fritz Roth fritz.roth at gmail.com
Mon Aug 22 13:32:46 PDT 2011


I'd be happy to sign up for FuncAssociate to participate in the standard.

Below is an example of our file output of basic results (which would 
need to be supplemented with metadata about the query list, analysis 
type and version info on GO annotation):

Cheers,
Fritz

OVERREPRESENTED ATTRIBUTES
N       X       LOD     P       P_adj   attrib ID       attrib name
4       4       4.260692768     1.35E-13        0       GO:0019136 
   deoxynucleoside kinase activity
2       2       3.913649889     4.45E-07        0       GO:0004797 
   thymidine kinase activity
2       2       3.913649889     4.45E-07        0       GO:0009153 
   purine deoxyribonucleotide biosynthetic process
2       2       3.913649889     4.45E-07        0       GO:0050145 
   nucleoside phosphate kinase activity
7       10      3.826424017     1.07E-21        0       GO:0019206 
   nucleoside kinase activity
11      47      3.557273674     2.11E-28        0       GO:0019205 
   nucleobase, nucleoside, nucleotide kinase activity
2       3       3.436503404     1.33E-06        0.001   GO:0009189 
   deoxyribonucleoside diphosphate biosynthetic process
2       3       3.436503404     1.33E-06        0.001   GO:0046940 
   nucleoside monophosphate phosphorylation
3       6       3.258069882     5.16E-09        0       GO:0009265 
   2'-deoxyribonucleotide biosynthetic process
2       4       3.214629422     2.67E-06        0.008   GO:0009215 
   purine deoxyribonucleoside triphosphate metabolic process
6       19      3.105207303     6.89E-16        0       GO:0015949 
   nucleobase, nucleoside and nucleotide interconversion
2       5       3.068476153     4.44E-06        0.011   GO:0009186 
   deoxyribonucleoside diphosphate metabolic process
3       8       3.061724766     1.44E-08        0       GO:0004017 
   adenylate kinase activity
3       8       3.061724766     1.44E-08        0       GO:0009151 
   purine deoxyribonucleotide metabolic process
4       12      3.03004196      6.66E-11        0       GO:0043174 
   nucleoside salvage
6       23      2.992402015     2.56E-15        0       GO:0019201 
   nucleotide kinase activity
3       9       2.989148861     2.16E-08        0       GO:0008655 
   pyrimidine-containing compound salvage
3       9       2.989148861     2.16E-08        0       GO:0009263 
   deoxyribonucleotide biosynthetic process
3       9       2.989148861     2.16E-08        0       GO:0043097 
   pyrimidine nucleoside salvage
2       7       2.872131036     9.33E-06        0.018   GO:0009133 
   nucleoside diphosphate biosynthetic process
3       12      2.824262889     5.66E-08        0       GO:0043101 
   purine-containing compound salvage
5       24      2.810656366     2.65E-12        0       GO:0043094 
   cellular metabolic compound salvage
2       8       2.799555131     1.24E-05        0.021   GO:0009200 
   deoxyribonucleoside triphosphate metabolic process
6       35      2.765314884     4.10E-14        0       GO:0072528 
   pyrimidine-containing compound biosynthetic process
5       27      2.74843268      5.03E-12        0       GO:0009262 
   deoxyribonucleotide metabolic process
4       21      2.716195603     8.03E-10        0       GO:0009394 
   2'-deoxyribonucleotide metabolic process
6       39      2.709990992     8.24E-14        0       GO:0016776 
   phosphotransferase activity, phosphate group as acceptor
3       15      2.705000746     1.17E-07        0       GO:0046134 
   pyrimidine nucleoside biosynthetic process
2       10      2.682999082     2.00E-05        0.032   GO:0046939 
   nucleotide phosphorylation
4       26      2.606924842     2.00E-09        0       GO:0009163 
   nucleoside biosynthetic process
6       63      2.47476085      1.70E-12        0       GO:0072527 
   pyrimidine-containing compound metabolic process
3       24      2.469245012     5.19E-07        0       GO:0006221 
   pyrimidine nucleotide biosynthetic process
4       38      2.420985013     9.84E-09        0       GO:0006220 
   pyrimidine nucleotide metabolic process
11      535     2.387304415     2.74E-16        0       GO:0055086 
   nucleobase, nucleoside and nucleotide metabolic process
4       44      2.351197379     1.81E-08        0       GO:0006213 
   pyrimidine nucleoside metabolic process
3       31      2.346661751     1.15E-06        0       GO:0006206 
   pyrimidine base metabolic process
5       62      2.340062276     3.98E-10        0       GO:0009112 
   nucleobase metabolic process
6       86      2.328050209     1.17E-11        0       GO:0009116 
   nucleoside metabolic process
8       175     2.283826823     4.62E-14        0       GO:0009165 
   nucleotide biosynthetic process
3       36      2.276335431     1.82E-06        0.002   GO:0006144 
   purine base metabolic process
8       190     2.246196442     9.01E-14        0       GO:0034404 
   nucleobase, nucleoside and nucleotide biosynthetic process
8       190     2.246196442     9.01E-14        0       GO:0034654 
   nucleobase, nucleoside, nucleotide and nucleic acid biosynthetic process
11      730     2.244914938     8.50E-15        0       GO:0016301 
   kinase activity
10      484     2.170755555     1.76E-14        0       GO:0006753 
   nucleoside phosphate metabolic process
10      484     2.170755555     1.76E-14        0       GO:0009117 
   nucleotide metabolic process
11      865     2.16666454      5.52E-14        0       GO:0016772 
   transferase activity, transferring phosphorus-containing groups
8       237     2.145476488     5.39E-13        0       GO:0018130 
   heterocycle biosynthetic process
10      633     2.048272307     2.59E-13        0       GO:0046483 
   heterocycle metabolic process
3       61      2.033591953     9.09E-06        0.017   GO:0009119 
   ribonucleoside metabolic process
8       367     1.947223391     1.81E-11        0       GO:0044271 
   cellular nitrogen compound biosynthetic process
11      1443    1.92666023      1.53E-11        0       GO:0005524 
   ATP binding
3       78      1.922370296     1.91E-05        0.028   GO:0009123 
   nucleoside monophosphate metabolic process
11      1467    1.918783408     1.83E-11        0       GO:0032559 
   adenyl ribonucleotide binding
11      1476    1.915859953     1.96E-11        0       GO:0030554 
   adenyl nucleotide binding
11      1644    1.864068833     6.36E-11        0       GO:0016740 
   transferase activity
11      1694    1.849578899     8.83E-11        0       GO:0044281 
   small molecule metabolic process
11      1773    1.827448102     1.45E-10        0       GO:0035639 
   purine ribonucleoside triphosphate binding
8       485     1.820897678     1.67E-10        0       GO:0044283 
   small molecule biosynthetic process
11      1803    1.819274035     1.75E-10        0       GO:0032555 
   purine ribonucleotide binding
11      1804    1.819003656     1.76E-10        0       GO:0032553 
   ribonucleotide binding
5       195     1.816455301     1.31E-07        0       GO:0006725 
   cellular aromatic compound metabolic process
11      1815    1.816038242     1.88E-10        0       GO:0017076 
   purine nucleotide binding
4       142     1.814717244     2.08E-06        0.003   GO:0072522 
   purine-containing compound biosynthetic process
11      2202    1.720607319     1.55E-09        0       GO:0000166 
   nucleotide binding
11      2614    1.633714078     9.98E-09        0       GO:0006139 
   nucleobase, nucleoside, nucleotide and nucleic acid metabolic process
6       410     1.61863627      1.43E-07        0       GO:0072521 
   purine-containing compound metabolic process
11      3014    1.559588304     4.68E-08        0       GO:0034641 
   cellular nitrogen compound metabolic process
11      3116    1.54195589      6.70E-08        0       GO:0006807 
   nitrogen compound metabolic process
5       376     1.521749164     3.37E-06        0.008   GO:0006163 
   purine nucleotide metabolic process
4       286     1.501470571     3.32E-05        0.042   GO:0009144 
   purine nucleoside triphosphate metabolic process
4       294     1.489137637     3.69E-05        0.047   GO:0009141 
   nucleoside triphosphate metabolic process
9       1964    1.325909583     5.10E-07        0       GO:0005829      cytosol
11      5059    1.266574184     1.22E-05        0.018   GO:0003824 
   catalytic activity
8       2091    1.137266187     1.46E-05        0.022   GO:0044249 
   cellular biosynthetic process
8       2211    1.109488516     2.23E-05        0.035   GO:0009058 
   biosynthetic process

UNDERREPRESENTED ATTRIBUTES
N       X       LOD     P       P_adj   attrib ID       attrib name


At 12:06 PM 8/22/2011, Gavin Sherlock wrote:
>Hi Chris,
>
>If it's relatively trivial, I'd be happy to add whatever is decided 
>upon to GO::TermFinder (which I need to make some updates to anyway).
>
>Cheers,
>Gavin
>
>On Aug 17, 2011, at 11:10 AM, Chris Mungall wrote:
>
> > Hi gofriends,
> >
> > Within the GO consortium we are considering providing a unified 
> interface to a number of heterogeneous term enrichment tools. In 
> order to facilitate this we would need to have a standard output 
> format and/or API for the tool results. I think the standardizing 
> on a format would be easier than an API.
> >
> > I asked this question on the biostar forum:
> > 
> http://biostar.stackexchange.com/questions/11269/is-there-a-standard-format-for-go-term-enrichment-results
> >
> > But I thought I would also ask here, as I know a number of tool 
> providers are subscribed.
> >
> > Thanks
> > Chris
> > _______________________________________________
> > go-friends mailing list
> > go-friends at lists.stanford.edu
> > https://mailman.stanford.edu/mailman/listinfo/go-friends
>
>_______________________________________________
>go-friends mailing list
>go-friends at lists.stanford.edu
>https://mailman.stanford.edu/mailman/listinfo/go-friends

____________________________________________________
Frederick P. (Fritz) Roth

Professor, Donnelly Centre for Cellular & Biomolecular Research, 
University of Toronto

Senior Scientist, Samuel Lunenfeld Research Institute, Mt. Sinai 
Hospital, Toronto

Lecturer, Biological Chemistry & Molecular Pharmacology Dept, Harvard 
Medical School

mailto:fritz.roth at gmail.com
http://llama.mshri.on.ca/
____________________________________________________  




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