How do you obtain a list of transcription factors from a genome?

Question

[DNAngel]

Hello all,

I am completely new to studying transcription factors and I've been wanting to try to find which TFs are enriched in a new genome my lab has recently processed. I know I can use a program called ASTRIX to do so, and I have transcriptome data that I can play with, but I cannot understand how to obtain a list of TFs associated with my species? I've only come across a database called JASPAR that seems to curate all the TFs but unfortunately my species is not there.

I can only assume that there are programs that will screen my genome and identify TFs for me based on the sequence - but for enrichment programs to work it should be a list of just TF names (not sequences).

I would appreciate anyone to just point me into the right direction or specific program for this. It looks like most other databases I come across are only for human or fruit fly and I am working with different bees, so my species is not there.

Answer 1

[ATpoint]

We usually use AnimalTFDB3 containing a large number of species.

[DNAngel]

This is like JASPAR in a sense it has the most commonly studied species. What to do if I am looking at a species not on this list? Am I to just use the next closest species? I am looking at bees (not honey bees which are mostly commonly studied) so I think the only thing I could maybe use is the fruit fly.

[LDT]

This is what I would do. I would go for the fly TFs

[DNAngel]

Ok I will try that. Thank you for the help.

Answer 2

[LDT]

and this one for plant species http://planttfdb.gao-lab.org/,

you can also use https://www.ebi.ac.uk/interpro/search/sequence/

Which one is your species? I would be careful with interposcan. I would find a closely related species that are in the database, and I would pick the TF factor based on homology

[DNAngel]

I would be looking at different bees - so I would most likely have to obtain a list of TFs from Drosophila as the closely related species. But I thought there would be a way to do that if I already have my species' genome - by scanning the genome for TFs etc.

[DNAngel]

Interpro scan requires that I already have TF sequences from my species - but I don't know how to get those from my genome. The only way I can think of is obtaining all the annotated genes and just manually scanning them for terms such as 'transcription factor". But this seems like I would just miss many TFs if they aren't already annotated.

[LDT]

yes this is what I would do with interPro scan, and indeed that's the disadvantage of interpro