Fig. 1

Inferring transcription factors activities from gene expression during TGFβ induced EMT in A-549 and MDA-231-D cell lines. A Flowchart depicting xcore and xcoredata functionalities. B Boxplots showing R² values for gene expression prediction models constructed using different molecular signature sets: Motif-based (Jaspar, SwissRegulon) and ChIP-seq based (ReMap2020, ChIP-Atlas). Each boxplot shows R² values pooled across all the replicates. Models were trained and evaluated in tenfold cross-validation on individual replicates, using data on gene expression changes between 0 and 24 h after treatment in our newly generated TGFβ induced EMT experiment performed in A-549 and MDA-231-D cell lines. C Heatmap showing the dynamics of TF activities during TGFβ induced EMT. Heatmaps on the left present TF activities estimated using CAGE data from our newly generated TGFβ induced EMT experiment performed on A-549 and MDA-231-D cell lines. Heatmap on the right depicts TF activities estimated using previously published microarray data from the TGFβ induced EMT experiment performed on A-549 cell lines. The TF activities were calculated in the reference to 0 h time point. Only the top-scoring ReMap2020 signatures are shown. Grey color designates NA values