decoupleR: Ensemble of computational methods to infer biological activities from omics data

We used decoupleR to evaluate the performance of individual methods by recovering perturbed transcription factors (TFs) from a curation of single-gene perturbation experiments (Holland et al., 2020). As a resource we used DoRothEA, a gene regulatory network linking TFs to target genes by their mode of regulation (Garcia-Alonso et al., 2019). Perturbation experiments where the targeted regulator was not in DoRothEA were removed. After filtering, this dataset is composed of gene expression data from 92 knockdown and overexpression experiments of 40 unique TFs in human cells. Additionally, we tested the performance of decoupleR on phospho-proteomic data. For this, we  filtered in a similar fashion a curated set of knockdown and overexpression single-kinase perturbation experiments, obtaining 63 experiments including 14 unique kinases, and applied a weighted resource from the same publication that links kinases to their target phosphosites (Hernandez-Armenta et al., 2017). For the transcriptomic dataset, differential expression analysis was performed with limma (Ritchie et al., 2015) and the resulting t-values were used as input. For the phospho-proteomics, the quantile-normalized log2-fold changes from different studies were used to make them comparable.