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Finding Transcription factors from a set of genes list

Hello all,

I have a list of 863 genes (mouse) after doing DEG analysis and i want to see the transcription factors primarily responsible for the expression of these genes. I have tried to use iRegulon but its showing error all the time. Are there any such tools that i can use to find the TFs? or any packages in R?

Thank you in advance.

And how to resolve this error enter image description here

rna-seq transcription factor degs
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updated by i.sudbery i.sudbery • written by rajdeepboral00 • rajdeepboral00

I looks from that error message that you are puting the wrong type of gene id into iRegulon.

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written by i.sudbery i.sudbery

As asked, i have put the gene MGI symbols, still its showing such errors.

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written by rajdeepboral00 • rajdeepboral00

1 answer

Take a look at ChEA3 from the Maayan lab. It is a library of TF-target interactions, and an algorithm to look for enrichments. If you use the interfact at https://maayanlab.cloud/chea3/ you will get a score for each transcription factor. Whereas, if you use the Enrichr interface, you will get statistically significant interactions.

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written by i.sudbery i.sudbery

Can i use the top ranked TFs from ChEA3 for my further analysis?

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written by rajdeepboral00 • rajdeepboral00

That is what we have done in the past. But I'd be careful to take this just as a hypothesis to be tested - particularly as any cut of would be arbitrary.

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written by i.sudbery i.sudbery

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