significant expressed genes in cuffdiff output

Question

[zizigolu]

Hi,

In cuffdiff output can I use all of genes in gene_exp.diff folder for knocking down or over-expressing assay or I should only manure on genes which signed with "yes" in significant column? Because some important genes in this list have "no" in significant column

Thank you

Answer 1

[Benn]

It depends on what you want in your experiment. What is your experimental design and aim of study?

If you have searched for significantly differentially expressed genes, and you want to show in a functional assay what the effect of knock down or overexpression would be, then yes take the significant genes assigned as "yes".