Identification of transcription factors from a list of DEGs

Question

[navamikrishna99]

Hello everyone,

I have a list of 245 DEGs . I separated it into unregulated and down-regulated based on Fc value

I want to know whether I need to separately analyze DEGs as (up-regulated or down-regulated) for identifying TFs

TFs for unregulated genes
TFs for downregulated genes

Or can I use the whole DEGs as together to identify TFs?

Which one is correct ?

Please help me ..

[Hyper_Odin]

Which tool are you using ?

[navamikrishna99]

I'm using Enrichr . My doubt is, should I analyze the upregulated and downregulated genes separately for identifying TFs ?

[Hyper_Odin]

Yes, You should separate the list in that case.

[navamikrishna99]

Thankyou so much Sir

Answer 1

[Collin]

You could also try the method Lisa2 to infer transcription factors (TFs) underlying DEG results (http://lisa.cistrome.org/ ). One advantage of Lisa2 is that it will have a broad range of TFs it can infer, as it uses 1,000's of ChIP-seq profiles from the cistrome database. You can also input the up-regulated and down-regulated genes into two separate lists (recommended approach) and then compare the results.

[navamikrishna99]

Thankyou for the suggestion Sir

Answer 2

[lieven.sterck]

Alternatively you can have a look at software like lemone (there are other similar tools around as well) that build transcriptional modules based on expression data (== they try to look for the TF that can explain the expression pattern in your data) , if I remember correctly.

[navamikrishna99]

Thankyou for the suggestion Sir. I will check it out .