Transcription factors and gene expression profile

Question

[biology_inform]

I have RNA-seq data and I would like to investigate alterations in gene expression profile due to its transcription factor change. In other words, I would like to do transcriptional network analysis of a specific cell line. For instance when a tf expression is upregulated which genes are enhanced further how pathways are changed. Is there a tool or something else which works for those? I appreciated your help in advance.

Answer 1

[Hamid Ghaedi]

It seems you are looking for regulon analysis: Network of genes and their corresponding regulators like TFs. The RTN package was designed to deal with this kind of question.

Answer 2

[R_newbie]

Some tools I have been used, IPA, chEA3