Question: How can I Find modules of a gene?
0
gravatar for hodatn
19 months ago by
hodatn0
hodatn0 wrote:

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

modules rna-seq plants • 613 views
ADD COMMENTlink modified 19 months ago by colindaven1.2k • written 19 months ago by hodatn0

Please expand your question to contain sufficient amount of detail.

ADD REPLYlink written 19 months ago by Michael Dondrup46k

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

ADD REPLYlink written 19 months ago by Renesh1.6k

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

ADD REPLYlink written 19 months ago by Michael Dondrup46k

Thank you. I explained more.

ADD REPLYlink written 19 months ago by hodatn0
0
gravatar for jrj.healey
19 months ago by
jrj.healey12k
United Kingdom
jrj.healey12k wrote:

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.

ADD COMMENTlink modified 19 months ago • written 19 months ago by jrj.healey12k

I explained more. Thanks

ADD REPLYlink written 19 months ago by hodatn0
0
gravatar for colindaven
19 months ago by
colindaven1.2k
Hannover Medical School
colindaven1.2k wrote:

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

ADD COMMENTlink written 19 months ago by colindaven1.2k
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