Question: Generating A Gene Ontology Network For Cytoscape
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gravatar for jav.cdp
6.4 years ago by
jav.cdp10
jav.cdp10 wrote:

Hello. I need help using cytoscape. I have a list of genes of interest that I use as input in STRING 9.0. Then I download a .xml file to use as network in Cytoscape. The next step is to import ontology and annotation to create a DAG. The problem here is the annotation file. I read the manual and I need to have a conection between the attributes in my protein interaction network (previously created) with the annotation file. I tried to use the annotation files that exists in Cytoscape and I create a new file with 2 columns: the gene name and the ontology. When I create the view of my DAG I donĀ“t see the information that I need. The labeI in my network is only the gene ontology IDs or information related with the ontologys (ex. the full name ontology). I need information of Uniprot IDs, or KEGG IDs to put in my network and exactly locate my proteins in the created DAG. I hope you can understand and help me. Thanks.

gene protein cytoscape ontology • 5.4k views
ADD COMMENTlink modified 6.4 years ago by Leandro Lima920 • written 6.4 years ago by jav.cdp10
1

AGAIN, this is the same question asked over the last week under the titles of Gene Ontology Programming, Gene Ontology Tree Programming, Input File For Ontology In Cytoscape, and Generating A Gene Ontology Network For Cytoscape. Can you please just use one question header?

I use Cytoscape quite often for network analysis and I have no idea what a DAG is? Can you clarify?

All your questions here are of the variety: I am having trouble and I need someone to tell me how to do this. The problem is it is very hard to understand what you want to do exactly. You are not asking a clear question. I suggest you do some serious reading about network analysis and make sure you know why you want to do this.

ADD REPLYlink modified 6.4 years ago • written 6.4 years ago by Josh Herr5.6k
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You really need to be more clear with your question like Josh said. From what I can gather, you are missing GO annotations for your list of genes? You are visualizing the GO network in cytoscape as a direct acyclic graph, but since you don't have GO annotations for your genes, you can't relate your genes of interest to the GO network? What organism are you working on?

ADD REPLYlink written 6.4 years ago by Damian Kao15k

im working with Helicobacter pylori. There is no annotations. I need to relate my genes with de gene ontologies and with other data base, such Uniprot or KEGG, and see it in my network.

ADD REPLYlink written 6.4 years ago by jav.cdp10
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You can blast your transcript sequences and use Blast2GO. You can also use gene ontology's external mapping indeces to relate KEGG/COG/EC... database IDs to go IDs: http://www.geneontology.org/GO.indices.shtml

ADD REPLYlink written 6.4 years ago by Damian Kao15k
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gravatar for Leandro Lima
6.4 years ago by
Leandro Lima920
San Francisco, CA
Leandro Lima920 wrote:

I recommend you to use APID2NET plugin for Cytoscape.

http://bioinfow.dep.usal.es/apid/apid2net.html

I think it's possible to perform the whole analysis you want.

And if you are not interested in gene networks, it's possible to use WebGestalt.

http://bioinfo.vanderbilt.edu/webgestalt/

ADD COMMENTlink modified 6.4 years ago • written 6.4 years ago by Leandro Lima920

The APID2NET plugin/app is not compatible with Cytoscape 3.0 is no longer supported as a plugin. I have used it in the past, but it's no longer functional.

ADD REPLYlink written 6.4 years ago by Josh Herr5.6k

They say it's compatible until version 2.6, but I had no problems using with version 2.8. With 3.0 I haven't tried. =(

ADD REPLYlink written 6.4 years ago by Leandro Lima920
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