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Differentially expressed genes Parharn Bioinformatics 11 03-04-2014 02:16 AM
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Old 03-04-2014, 08:42 AM   #1
Parharn
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Default Profiling differentially expressed genes

Hi,
I am new to RNA-seq field. I managed to successfully find differentially expressed genes between to conditions. They are like couple of thousands. I am sure there are softwares out there that categorize and find the relations between them rather than looking them up one by one myself. So how do you approach it? Which softwares do you recommend?

Thanks,
Parham
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Old 03-04-2014, 10:05 AM   #2
DonDolowy
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Tjenar tjenar,

you could either run GSEA on the dataset to see what gene sets are enriched in your conditions or you could go for GO analysis on your differentially expressed genes.

Last edited by DonDolowy; 03-05-2014 at 05:05 AM.
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Old 03-05-2014, 05:03 AM   #3
Parharn
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Tjenare,
Danke schön. I will try GSEA. Is there any other software you know of?

Last edited by Parharn; 03-05-2014 at 05:06 AM.
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Old 03-05-2014, 05:06 AM   #4
DonDolowy
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Yep, check out http://www.broadinstitute.org/gsea/
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