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Old 01-17-2012, 11:22 PM   #1
scami
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Default Pathway mining

Hi there,

I have a list of genes that are differently represented in two organisms of the same species. Is there a software that will allow me to understand whether these genes (or a sub-group) belong to the same biological pathway?

thanks for the help
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Old 01-18-2012, 02:53 AM   #2
Robby
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Hi Scami,

cou can try for example BioMyn or Skypainter:
http://www.biomyn.de
http://www.reactome.org/cgi-bin/skypainter2

But I am sure, that there are many other tools. Maybe someone else has some suggestions?!

Best regards
Robby
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Old 01-18-2012, 03:01 AM   #3
simonandrews
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We use David quite a bit:

http://david.abcc.ncifcrf.gov/

The clustering of related groups tends to make interpretation easier.
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Old 01-18-2012, 05:03 AM   #4
scami
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Thanks guys I will have a look at both of them shortly!
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Old 01-18-2012, 05:43 AM   #5
turnersd
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You might also see:

GeneMania: http://genemania.org/
GOrilla: http://cbl-gorilla.cs.technion.ac.il/
amiGO: http://amigo.geneontology.org/cgi-bin/amigo/go.cgi
WebGestalt: http://bioinfo.vanderbilt.edu/webgestalt/
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Old 01-18-2012, 08:11 AM   #6
Assaf
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Spike, exapnder and others pathways analysis tools:
http://acgt.cs.tau.ac.il/index.php

pandora:

http://www.pandora.cs.huji.ac.il/
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Old 01-18-2012, 08:26 AM   #7
turnersd
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To invigorate this discussion a bit, how do you choose between all these free web apps (and other commercial apps like IPA) that do pathway analysis, overrepresentation analysis, GO enrichment, etc? What criteria do you use? What do you look for?
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Old 01-24-2012, 10:58 AM   #8
bkmacy
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You might also consider Ingenuity iReport at http://www.ingenuity.com/getireport/ Upload your RNA-Seq CuffDiff files at http://www.ingenuity.com/getireport/ and get a free preview of your data in the iReport
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Old 01-24-2012, 11:17 AM   #9
turnersd
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Quote:
Originally Posted by bkmacy View Post
You might also consider Ingenuity iReport at http://www.ingenuity.com/getireport/ Upload your RNA-Seq CuffDiff files at http://www.ingenuity.com/getireport/ and get a free preview of your data in the iReport
At $500 per dataset, iReport is pretty steep.
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Old 01-24-2012, 11:24 AM   #10
adaptivegenome
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Quote:
Originally Posted by bkmacy View Post
You might also consider Ingenuity iReport at http://www.ingenuity.com/getireport/ Upload your RNA-Seq CuffDiff files at http://www.ingenuity.com/getireport/ and get a free preview of your data in the iReport
You have only made two posts on SEQanswers and both advertise this report. Please refrain from advertising on the board via posts or your posts might get flagged in the future.
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Old 03-12-2012, 02:49 PM   #11
daniele.merico
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Another tool that's worth checking out is GSEA (Subramanian et al), if you think you can meaningfully rank your genes.

Once you have picked your pathway analysis tools, you can use this Cytoscape plugin for visualization: http://baderlab.org/Software/EnrichmentMap

If you have some time, I would also recommend a look at the more methodological literature about potential biases you may hit when you do a gene-set enrichment analysis (as suggested by another post).
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Old 03-12-2012, 05:09 PM   #12
turnersd
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In addition to the comments I and others left above, I wrote a blog post about this at Getting Genetics Done. I tried to give some examples and code to run analysis in free, open-source software.
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Old 03-13-2012, 03:46 AM   #13
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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.
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Old 03-13-2012, 04:39 AM   #14
severin
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Quote:
Originally Posted by turnersd View Post
In addition to the comments I and others left above, I wrote a blog post about this at Getting Genetics Done. I tried to give some examples and code to run analysis in free, open-source software.
Nice blog post.
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Old 05-15-2012, 12:52 PM   #15
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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

Last edited by billstevens; 05-15-2012 at 12:55 PM.
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Old 05-15-2012, 12:55 PM   #16
billstevens
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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
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Old 05-15-2012, 07:19 PM   #17
billstevens
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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?
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Old 05-16-2012, 05:48 AM   #18
turnersd
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Bill - have you used GOSeq with your RNA-seq data?
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Old 05-17-2012, 03:15 AM   #19
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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
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Old 05-18-2012, 09:12 AM   #20
Tom Bair
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Default 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

Last edited by Tom Bair; 05-18-2012 at 09:19 AM. Reason: Addition
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