I need to understand the dynamics of transcription factor expression in the RNA-Seq data. Is there any tool to identify the transcription factors from the RNA-Seq data. Also suggest me tools for constructing the network of interaction pathways from RNA-Seq data.
What species are you working with?
Can't you simply GO annotate your genes and select for a relevant GO term, like GO:0003700 (sequence-specific DNA binding transcription factor activity).
If you plan to annotate your genes with GO terms, I recommend using CLC Genomics. Using the BLAST2GO function, you are able to create a combined graph which shows all the different levels of GO Terms and how they interconnect. You can also create individual pie charts to analyze the percentage of each type of GO Term at different levels. You can learn more about it here: https://www.blast2go.com/b2g-plugins/clcbio-plugin
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