[billstevens]

Anyone else finding Cytoscape very difficult to work with? When I try to load anything over 125 genes, it won't show up. Additionally, a lot of the documentation seem to match up with older versions of Cytoscape, but not the new version Cytoscape 2.8.3. Including Cytoprophet. Any ideas?

Totally Frustrated

[billstevens]

Additionally, anyone out there using GSEA with RNA-SEq? I worked pretty darn hard to get everything in their right format, got in there, and now when I want to run the GSEA, I have no idea which Gene Set to pick, and there is no documentation whatsoever to help you figure out which one to choose. It won't match the dataset. Any ideas how to get this to work?

[turnersd]

Bill - have you used GOSeq with your RNA-seq data?

[choishingwan]

Bill, I guess you might be able to solve the problem of Cytoscape not showing anything by increasing the allowed ram for the programme. You may do that by following the instruction on Cytoscape's webpage: http://wiki.cytoscape.org/How_to_inc..._for_Cytoscape

[Tom Bair]

RNA-Seq length bias

Just be aware that using microarray designed tools may not be the best option

Bioinformatics. 2011 Mar 1;27(5):662-9

And some others show a length bias in RNA-seq results which can carry forward to enriched pathway or ontology results just based on the fact that they contain longer than average genes.

Maybe someone with more knowledge than I can comment further, but here is a tool that claims an RNA-seq corrected approach http://genomebiology.com/2010/11/2/R14

[chknbio]

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?

Thanks!

[Jane M]

Hello,

I spent the afternoon yesterday, looking for a free pathway analysis tool. I checked the ones suggested here and here: http://seqanswers.com/forums/showthread.php?t=9349 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,
Jane

[yksikaksi]

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.