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Adding Go Annotation In Cytoscape

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

cytoscape gene
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updated by Gjain Gjain • written by Woa Woa

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

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written by Khader Shameer Khader Shameer

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

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written by Woa Woa

1 answer

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

enter image description here

• 3 views • link
written by Gjain Gjain

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

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written by Woa 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?

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written by Woa Woa

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