Question: How can I Find modules of a gene?
0
gravatar for hodatn
2.3 years 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 • 809 views
ADD COMMENTlink modified 2.3 years ago by colindaven1.9k • written 2.3 years ago by hodatn0

Please expand your question to contain sufficient amount of detail.

ADD REPLYlink written 2.3 years ago by Michael Dondrup47k

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

ADD REPLYlink written 2.3 years ago by Renesh1.8k

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

ADD REPLYlink written 2.3 years ago by Michael Dondrup47k

Thank you. I explained more.

ADD REPLYlink written 2.3 years ago by hodatn0
0
gravatar for Joe
2.3 years ago by
Joe16k
United Kingdom
Joe16k 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 2.3 years ago • written 2.3 years ago by Joe16k

I explained more. Thanks

ADD REPLYlink written 2.3 years ago by hodatn0
0
gravatar for colindaven
2.3 years ago by
colindaven1.9k
Hannover Medical School
colindaven1.9k 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 2.3 years ago by colindaven1.9k
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