The CollecTRI-derived regulons contain signed transcription factor (TF) - target gene interactions compiled from 12 different resources. This collection provides an increased coverage of transcription factors and was benchmarked against other known GRNs, showing a superior performance in identifying perturbed TFs based on gene expression data using the knockTF data sets.
The CollecTRI regulons are available in the DoRothEA and decoupler packages through OmniPath. A tutorial on how to perform TF activity estimation using CollecTRI is available in R and python.
To load the CollecTRI regulons through R or python you can use the following lines:
# processed regulons
decoupleR::get_collectri(organism='human', split_complexes=FALSE)
# raw regulons
OmnipathR::collectri(organism=9606L, genesymbols=TRUE, loops=TRUE)# processed regulons
import decoupler as dc
dc.get_collectri(organism='human', split_complexes=False)
# raw regulons
import omnipath as op
op.interactions.CollecTRI.get(genesymbols=True, organism=9606L, loops=True)ExTRI, HTRI, TRRUST, TFActS, IntAct, SIGNOR, CytReg, GEREDB, Pavlidis, DoRothEA A, NTNU curations
For more information about the CollecTRI-derived regulons, please check out the following scripts:
If you are interested in the construction of the CollecTRI meta-resource check out this repository
The CollecTRI-derived regulons are freely available. The original licenses of all resources included in CollecTRI can be found here
Müller-Dott, S., Tsirvouli, E., Vazquez, M., Ramirez Flores, R. O., Badia-I-Mompel, P., Fallegger, R., Türei, D., Lægreid, A., & Saez-Rodriguez, J. (2023). Expanding the coverage of regulons from high-confidence prior knowledge for accurate estimation of transcription factor activities. Nucleic Acids Research. https://doi.org/10.1093/nar/gkad841
