How can I Find modules of a gene?

Question

[hodatn]

I'm working on Transcription factors involved in secondary metabolite. This plant doesn't have whole genome sequence, So we did RNA-seq analysis for it. From RNA-seq analysis and data, now, I have a list of Transcription factors which are involved in secondary metabolites. I want to find the modules of these TFs and the TFs targets. Is there any software or database? I hope my explanation gives you sufficient amount of information, if it's not, please let me know. thank you

[Michael]

Please expand your question to contain sufficient amount of detail.

[Renesh]

Do you mean CDS, UTR regions of genes? For these you can use GFF file for respective plant species.

[Michael]

Modules could also refer to network analysis, please let's not speculate. The question will be closed anyway if not expanded.

[hodatn]

Thank you. I explained more.

Answer 1

[Joe]

I assume this means genes and any surrounding genes within an operon typically?

One such tool, which looks for the local neighbourhood of a gene is MultiGeneBlast

EDIT, as Michael said, we need more info, and I've just noticed the question is tagged with RNAseq so my answer probably isn't relevant.

[hodatn]

I explained more. Thanks

Answer 2

[colindaven]

Interproscan is a really good tool for running and integrating results from many different functional analysis tools. I think that is what you are looking for. You can get it from github, and I would recommend running it on a single machine, not a cluster