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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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Results of TF activites #16

Closed Semple-bio closed 3 years ago

Semple-bio commented 3 years ago

In part "04_TranscriptionFactor_activity_with_Dorothea", how are the TF activities calculated? Or, what does it mean if a TF has a high or low NES? Wouldn't it mean that the associated genes are mostly changed in that direction? When I plot (volcano_nice) my 3 topmost TFs' regulons, 2 of them has almost exclusively downregulated genes, and from the bottom-most 3 TFs' regulons, one has almost exclusively upregulated genes.

Also in the tutorial dataset the downregulated TF's (ZNF263) regulon has much more upregulated genes than downregulated.

rosherbal commented 3 years ago

Hi @Semple-bio, We calculate the TF activities with DOROTHEA. Check the bioconductor package or the github site to learn more about it.

Semple-bio commented 3 years ago

I did so. But I'm not sure how to interpret these results when I get conflicting results as written above.

gabora commented 3 years ago

Hi, jumping in the conversation;) Please check the mode of action! The activity is calculated based on the expression of the target genes, but also taking into account if the TF up or downregulates the expression!

Semple-bio commented 3 years ago

Thanks, now it starts to make sense :)