transcription factor database

Question

[Kurban]

Hello guys,

Is there any database where I can download transcription factor's sequences, like if I want to download all the known transcription factors sequences of Tribolium castaneum (let's say), how can I do that?

i wanna compare them with a transcriptome in a fasta file.

Answer 1

[pld]

For the beetle you mentioned it doesn't look like there's a dedicated resource, in general this isn't exactly trivial. You could use BioPython/Java/etc or entreztools and download by searching for specific terms, however the success of this depends on the completion and quality of the annotations available. You could also download in bulk and see if there are annotations you can filter on.

The other approach would be to get a list of known TFs from a related species and blast them against the genome of your species keeping hits. You could also do your own Pfam annotations to double check.

If your transcriptome is already annotated, couldn't you look in your data?

What are you planning to do when you 'compare'? There's the likelihood that many TFs will have multiple copies in the genome. You also have the risk of very similar paralogs (e.g. zinc finger TFs). There can be very high homology, but subtle differences at the sequence level can create large differences in the binding motif, which can confound your ability to determine what may be regulating what.

Depending on the tissue and even cell population(s) used, you may run into problems trying to determine if the expression of a TF is impacting the expression of another transcript. Without prior knowledge of the regulatory mechanism of that gene you can only see if there are correlations over time/condition. It is a start, but not the greatest. If your transcriptome came from material with multiple cell types, you may encounter conflicting results due to cell type-specific gene expression.

I've wanted to try a similar analysis for some time, but this isn't easy with a small transcriptome datasets and little/no knowledge of regulatory pathways.

[Kurban]

Hi @joe.cornish826,

Thanks for the tips, this isn't easy.