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saezlab / transcriptutorial

This is a tutorial to guide the analysis of RNAseq dataset using footprint based tools such as DOROTHEA, PROGENY and CARNIVAL
https://saezlab.github.io/transcriptutorial/
GNU General Public License v3.0
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Comparing Cancer cell lines with normal tissues #43

Closed RzgarHosseini closed 2 years ago

RzgarHosseini commented 2 years ago

Hi all,

I think in some part of the pipeline (e.g. DORothEA based TF-activity inference step), a differential gene-expression analysis has been performed. My question is that how cancer cell lines have been compared against normal tissues? Do you usually use TCGA match-normal for this purpose? or GTEX expression profiles of normal tissues? (e.g. https://ucsc-xena.gitbook.io/project/how-do-i/tumor-vs-normal) I guess you usually use Limma for differential gene expression analysis. Am I right? I assume that you have obtained the RNA-Seq profiles of the cancer cell lines from CellModelPassport?

Many thanks for your response in advance

Best, SRH

RzgarHosseini commented 2 years ago

Don't worry, be happy

adugourd commented 2 years ago

HI, sorry for the delay.

the data in the tutorial comes from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119931

We use limma for differential analysis, comparing WT and KO.

Cheers,

Aurelien