Adding Go Annotation In Cytoscape

Question

[Woa]

I've some Mouse protein interaction data. The nodes are named by their Uniprot ID and in the *.sif file the interactions appear like this:

• uniprotkb:Q80Y17 - uniprotkb:Q9JK84
  uniprotkb:Q80Y17 - uniprotkb:Q62074
  uniprotkb:Q80Y17 - uniprotkb:Q9JK83

After loading the sif file in Cytoscape v2.8 I wish to add GO annotation to the individual nodes. However all my attempts failed when using the online gene association information.

Can anybody tell me what 'primary key'/'Key attribute for network values' I've to consider.

I tried the yeast example and that runs fine.

Thanks

I followed these two instructions:

http://www.cytoscape.org/manual/Cytoscape2_6Manual.html#Import%20Ontology%20and%20Annotation

http://genmapp.org/GOLayout/GOLayout.html

[Khader Shameer]

Have you tried after removing "uniprotkb:" from your CIF file ?

[Woa]

Yes, tried that too but didn't help :(

Answer 1

[Gjain]

try BINGO http://www.psb.ugent.be/cbd/papers/BiNGO/Home.html

Update (Feb 2017): I have used ClueGO now which is pretty good.

Paper: ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

[Gjain]

I don't have a lot of experience with GORetriever but I think you can parse the uniprot entries using GORetriever -(http://agbase.msstate.edu/cgi-bin/tools/goretriever_select.pl) for GO terms. Please let me know if that is helpful.

[Woa]

Bingo works after the "uniprotkb:" prefixes were stripped. However, for MANY proteins Bingo was not able to identify the GO process, even though GO annotaion exists in the corresponding Uniprot entries. Is there any way to bypass this problem? Thanks

[Woa]

Thanks. And is there a good way I can add this extracted GO information as node attribute in a SIF file that cytoscape recognizes?