Hi,
I did analyzed a receptor gene for transcription factor binding sites and I found some transcription factors now I wanted to do further analysis. I would like to take suggestion regarding what I can do with this data towards a meaningful publication? also I would appreciate the help towards transcription factor regulatory network with these transcription factors. If anybody willing to help me I can plan meetings further to discuss in more details.
Hello,
Thinking of a meaningful publication, that depends a lot on what field or organism you are working. Briefly, I would think of studying those genes and understanding their precise known function. After that, I would think of every possible relation between their biological functions and your targeted gene. You could possibly expand that analysis for searching other genes putatively regulated by those transcription factors. This depending on your biological question, quality of genome annotation, and knowledge of consensus sequences for those TF. But anyway, you would want to proceed twards describing presumable compensatory mechanisms involving such concerted regulation of TF in response to their signaling pathways and biological responses in gene expression (including your target). Validating those results by RT-qPCR would be important. Looking for transcriptome libraries that might involve modulation in those genes, even for other species, might be of some help. You can check for a possible network using STRING. You could also try using KEGG pathways for visually plotting your data, or construct your own regulatory model.
Indeed, I believe you may have to increment your analysis in some ways in order to bring more consistency to your data. I am also working with TF right now, and I would say for you to think mostly about biological processes that are regulated in response to stimuli through distinct but interconnected pathways. Know your Biology first, that's the thing. Understand your model organism, and understand the processes you're dealing with.
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