Gene set enrichment analysis cuffdiff output

Question

[1769mkc]

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 .

Answer 1

[EagleEye]

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

Answer 2

[BioinfGuru]

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

[1769mkc]

can you suggest me a way to do ranking ?

[BioinfGuru]

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

Answer 3

[Sreeraj Thamban]

GO analysis using topGO Arabidopsis You can follow this thread.