Transcription factor

Question

[rheab1230]

Can anyone tell me how to find out the expression of TF in a cell lines using RNA-seq datasets?

Answer 1

[heskett]

This is such a common task that there will be dozens of walkthroughs and tutorials already posted in many places online! A quick google search for "rna-seq tutorial" will really help you here, but here's one for example.

https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html

[rheab1230]

Thank you for the link.

Answer 2

[jared.andrews07]

The same as you would for any other gene. You're going to have to be more specific. Which cell lines? Do you already have the data in hand? If so, what format is it in?

My best answer to so general a question is to read through a good workflow that explains each step thoroughly. Bioconductor has an excellent one.

[rheab1230]

the cell line is DU145. I have rna-seq data for DU145 cell lines. I have done chip-seq analysis followed by motif enrichment analysis to predict the enhancer. Now I have to find the expression of TF in DU145 cell lines and see which one is the major regulator.