Transcription factors and gene expression profile
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6 weeks ago

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 furtherly how pathways are changed. Is there a tool or something else which works for those? I appreciated your help in advance.

rna-seq Transcription expression factors profile gene • 334 views
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Entering edit mode
6 weeks ago
Hamid Ghaedi ★ 2.0k

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.

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6 weeks ago
R_newbie • 0

Some tools I have been used, IPA, chEA3

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