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Gene set enrichment analysis cuffdiff output

I have done cuffdiff analysis now I want to go for Gene set enrichment analysis .Any suggestion how do I proceed from the cufdiff output for Gene set enrichment analysis , any suggestion or ways to do it would be really helpful .

rna-seq
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updated by Sreeraj Thamban Sreeraj Thamban • written by 1769mkc 1769mkc

3 answers

You can extract the 'gene_name' (Gene Symbols) from your file and perform GO term or KEGG pathway enrichment analysis using GeneSCF.

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written by EagleEye EagleEye

You could extract the set of differentially expressed genes from the gene_exp.diff file and then use that list of genes as input in gprofiler

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written by BioinfGuru BioinfGuru

can you suggest me a way to do ranking ?

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written by 1769mkc 1769mkc

ranking = ordering

Order the file by significance (e.g. P-value, Q-value, or FDR) or change of expression (e.g. log fold change)

For example:

- Order a file of 1000 genes by q-value
- Gene x is first in the list because it has lowest p-value and is therefore rank 1
- Gene y is last in the list because it has the highest p-value and is therefore rank 1000
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written by BioinfGuru BioinfGuru

GO analysis using topGO Arabidopsis You can follow this thread.

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written by Sreeraj Thamban Sreeraj Thamban

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