Figure 1

CellFateScout study workflow. A) Validation pipeline. For each small molecule considered, we collected publicly available differential gene expression data describing its effect, information about its targets in STITCH, and a functional network. Using CellFateScout and other bioinformatics tools, we predicted the signaling pathways that it activates and evaluated how much closer these are to its known targets in the network, compared to randomly generated pathways. B) We combined gene expression data taken from the Connectivity Map project, information about small molecules targets from STITCH and functional networks from STRING to perform a systematic search with CellFateScout for active pathways triggered by small molecules and stored them in the Small Molecule Mechanisms Database. C) As input for active signaling pathway discovery, a functional network and a differential expression data set featuring two conditions A and B are needed. The discovered active pathways are shown in a Cytoscape network view and used to query the Small Molecule Mechanisms Database for matching signaling pathways triggered by small molecules. The resulting small molecules are then listed in a result table and we can highlight edges and nodes that are shared between the active pathways found by CellFateScout and the active pathways triggered by small molecules.