Question: transcription factor binding sites were not over represented in modules
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gravatar for beiki.h.m
5.3 years ago by
beiki.h.m10
Belgium
beiki.h.m10 wrote:

Hello, my name is Hamid, I have constructed a condition independent gene co-expression network. There are some transcription factors in modules of this network. The function of these transcription factors are in accordance with the module function, but their binding sites were not over represented in that module. I would be very happy if somebody help me to find an explanation for this problem?

Vertebrates known transcription factor binding motifs were downloaded from the JASPAR database. Overrepresentation of known transcription factor binding motifs in the CIS regions of the genes within each module was performed using Clover.

Thanks in Advance

ADD COMMENTlink written 5.3 years ago by beiki.h.m10

In what genomic region did you search? Searching TF binding sites using sequence motifs is nice in theory but usually doesn't work in practice since the search space is large and they're found everywhere.

ADD REPLYlink written 5.3 years ago by Asaf8.4k

Dear Asaf

Thanks to your response, I constructed Soy bean scale free gene interaction network using integration of gene expression datasets derived from diverse range of microarray experiments, including different tissues and experimental conditions.

ADD REPLYlink written 5.3 years ago by beiki.h.m10

As far as I know, these genes are co-expressed under different conditions and different tissues. So if a transcription factor included in the network module, its target should be included too. Do you agree?

 

ADD REPLYlink written 5.3 years ago by beiki.h.m10

Not necessarily, it might have a secondary effect and not drive the expression of the module. I'd try motif searching in promoters of the genes in the module as well (using MEME for instance) compared to other modules (discriminating search), maybe you'll get a common motif and find the main TF (though I doubt it).

ADD REPLYlink written 5.3 years ago by Asaf8.4k

Can you please explain more about

it might have a secondary effect

ADD REPLYlink modified 11 months ago by RamRS30k • written 5.3 years ago by beiki.h.m10

Dear Asaf thanks to your comments. they were very useful for me. Regards, Hamid

ADD REPLYlink written 5.3 years ago by beiki.h.m10

It means that the regulator might not influence the genes in the module but genes in another module.

ADD REPLYlink written 5.3 years ago by Asaf8.4k

Dear Asaf

I find the answer of my question. many thanks to your help.

ADD REPLYlink modified 11 months ago by RamRS30k • written 5.3 years ago by beiki.h.m10
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