Question about estimating TF activity

saezlab / CollecTRI

Gene regulatory network containing signed transcription factor-target gene interactions

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Question about estimating TF activity #6

Closed joan-yanqiong closed 1 year ago

joan-yanqiong commented 1 year ago

Hi there,

I've been using dorothea to estimate TF activity, but since CollecTRI has a bigger coverage I was wondering if I could estimate the TF activity with this database too. I read in the paper that you used binding weights to infer the activity, are these available too?

Best, Joan

smuellerd commented 1 year ago

Hi @joan-yanqiong!

Sorry for the late response. We do provide one of the weighted networks (FIMO_1000bp_raw.csv) in our Zenodo repository: https://zenodo.org/record/7773985#.ZCSMiexBw-Q which you can directly download. However, if you would be interested in any other of the weighted CollecTRI regulons (e.g. calculated for a different window frame) you can follow the scripts 04.1, 04.2 and 04.3 here: https://github.com/saezlab/CollecTRI/tree/main/scripts/CollecTRI.

Best Sophia