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Old 05-25-2012, 11:53 AM   #21
Location: Baltimore

Join Date: May 2012
Posts: 14

I have a list of DE genes in chicken tumor samples retrieved from a cuffdiff analysis. I would like to determine if these genes are part of a pathway. Does anyone have a recommendation for a program or web app to use for determining the pathway of RNAseq genes in the chicken?

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Old 05-26-2012, 03:35 AM   #22
Jane M
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Location: Paris

Join Date: Aug 2011
Posts: 239


I spent the afternoon yesterday, looking for a free pathway analysis tool. I checked the ones suggested here and here: and some others...

Nevertheless, I haven't found a tool fitting my needs, although what I want to do is very simple. I think I missed something or I'm doing something wrong...

I've found potential somatic mutations in leukemic cells for several patients. For each patient, I've a list of "mutated" genes. I only want to know in which pathways the genes are (mainly) involved.

The problem with the tools I tried is that I was asked for geneID from agilent... but I only have gene names: TET2, SRSF2,KRAS, NRAS...

Do there exist such tools using directly gene names or do I have to find the IDs in some databases to be able to use the other softwares?

Thank you for your help,
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Old 09-14-2012, 06:07 AM   #23
Location: Scandinavia

Join Date: Dec 2009
Posts: 20

Originally Posted by swaraj View Post
Cytoscape and its three plugins
1. Cytoprophet (Interaction network building)
2. BINGO (GO mapping for interaction network network)
3. VistaClara (Visualising interaction network expression pattern)

are very useful. A bit tricky to configure but my past experience with them has been highly fruitful for my research.
Do you have experience to work with the non model species onCytoscape? I have RNA-Seq data of non model species and I would like to do the biological pathway analysis, Cytoscape came to my mind as I heard that tool years ago.

Last edited by yksikaksi; 09-14-2012 at 06:08 AM. Reason: typo
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