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
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.
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