Question: Adding Go Annotation In Cytoscape
0
gravatar for Woa
8.1 years ago by
Woa2.7k
United States
Woa2.7k wrote:

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

gene cytoscape • 2.6k views
ADD COMMENTlink modified 8.1 years ago by Gjain5.3k • written 8.1 years ago by Woa2.7k

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

ADD REPLYlink written 8.1 years ago by Khader Shameer18k

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

ADD REPLYlink written 8.1 years ago by Woa2.7k
0
gravatar for Gjain
8.1 years ago by
Gjain5.3k
Munich, Germany
Gjain5.3k wrote:

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

ADD COMMENTlink modified 2.5 years ago • written 8.1 years ago by Gjain5.3k
1

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.

ADD REPLYlink written 8.1 years ago by Gjain5.3k

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

ADD REPLYlink written 8.1 years ago by Woa2.7k

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

ADD REPLYlink written 8.1 years ago by Woa2.7k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1138 users visited in the last hour