Step 2: Pathway analysis
Step 1 resulted in a set of transcription factors (TFs), that are likely repsonsible for the differential regulation of the observed set of DEGs. From available pathway data, we have extracted information about all relevant signaling cascades that regulate the activity of TFs; optimally, the TRANSPATH® database is used for this and the further analysis.
As has been proven in a large number of use cases, these pathways usually converge in a couple of key nodes, which qualify as candidate master regulators of the process under study.
Activities of transcription factors (TFs, blue circles) are regulated by upstream signaling cascades (components shown as green circles). These converge in certain nodes, representing molecules that are potential master regulators of the process under study.