Question: Gene set enrichment analysis cuffdiff output
0
gravatar for krushnach80
10 months ago by
krushnach80280
krushnach80280 wrote:

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 • 521 views
ADD COMMENTlink modified 10 months ago by Sreeraj Thamban90 • written 10 months ago by krushnach80280
4
gravatar for EagleEye
10 months ago by
EagleEye5.0k
Sweden
EagleEye5.0k wrote:

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

ADD COMMENTlink written 10 months ago by EagleEye5.0k
2
gravatar for YaGalbi
10 months ago by
YaGalbi1.1k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.1k wrote:

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

ADD COMMENTlink written 10 months ago by YaGalbi1.1k

can you suggest me a way to do ranking ?

ADD REPLYlink written 10 months ago by krushnach80280

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
ADD REPLYlink modified 10 months ago • written 10 months ago by YaGalbi1.1k
0
gravatar for Sreeraj Thamban
10 months ago by
Indian Institute of Science Education and Research
Sreeraj Thamban90 wrote:

GO analysis using topGO Arabidopsis You can follow this thread.

ADD COMMENTlink written 10 months ago by Sreeraj Thamban90
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