Question: Uniprot Ids To Go Pie Chart (And Interpro)
2
gravatar for cdsouthan
6.3 years ago by
cdsouthan1.8k
cdsouthan1.8k wrote:

Is there a simple web interface I can input UniProt IDs (up to 10K) and get back GO pie charts ? Maybe even the same type of chart for InterPro IDs as well ?

uniprot go • 3.9k views
ADD COMMENTlink modified 6.3 years ago by munch300 • written 6.3 years ago by cdsouthan1.8k

The question is what are GO pie charts? Protein belong to multiple GO categories so the pie chart will not sum to 100%...

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by David730

1) to David - yes but I'm primarily interested in comparing lists so submerging multiples is not so serious (so long as its standardised)

2) Having checked similar posts I found plotting a pie-chart of molecular function using gene ontology method? from 15 months back

3) This pointed me to Panther http://www.pantherdb.org/ which does substancialy what I need nicely - I would prefer species agnosticism but human is OK

4) Other tools like this would be of interest (even to check they gave aproximately the same results)

5) I'd really like to do the same with InterPro IDs and EC numbers but I guess there is a nesting and multiples issue there as well

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by cdsouthan1.8k

Instead of telling you how to do this I am going to ask why do you want it, and have you thought about what the data will tell you? There are some good reasons why we don't provide this functionality on the browse by GO term at http://www.uniprot.org/browse/uniprot/by/go/?query=#8150 while we do have it for http://www.uniprot.org/browse/uniprot/by/taxonomy/?query= . The main reason being that such a chart will tell you very little biologically and in practice can at most tell you about annotation priorities.

ADD REPLYlink written 6.3 years ago by Jerven640

For the record, (comparative) annotation priorities are exactly what I am after (OK I should have added this at the outset). The protein ID lists I am looking to compare are from drug mapping databases, including those that have cross-references in UniProt (DrugBank, BindingDB and ChEMBL) as an update to previous work (http://www.ncbi.nlm.nih.gov/pubmed/22821596)

Given the convenience and useful options of http://www.pantherdb.org/ this does all I need just now but I am well aware of the caveats associated with list comparison in this way

ADD REPLYlink modified 6.3 years ago • written 6.3 years ago by cdsouthan1.8k
1
gravatar for munch
6.3 years ago by
munch300
Munich
munch300 wrote:

I have created such GO pie charts in Cytoscape with the ClueGO (http://www.ici.upmc.fr/cluego/) plugin. A possible input format for the tool are UniProt IDs. If you need help with the tool fell free to write me. Here is a example GO pie chart created with ClueGO:

GO pie charts created with ClueGO

Maybe you can mapping the InterPro identifier to Uniprot? http://www.uniprot.org/help/mapping

ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by munch300

Thanks a lot for this useful answer

ADD REPLYlink written 6.3 years ago by cdsouthan1.8k

For the record I now use PANTHER

ADD REPLYlink written 3.7 years ago by cdsouthan1.8k
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