Abstract
Cell signaling pathways are sequences of biochemical reactions that propagate an input signal, such as a hormone binding to a cell-surface receptor, into the cell to trigger a reactive process. Assessment of pathway activities is crucial for determining which pathways play roles in disease versus normal conditions. To date various pathway flow/perturbation assessment tools are available, however they are constrained to specific algorithms and specific data types. There are no accepted standards for evaluation of pathway activities or simulation of flow propagation events in pathways, and the results of different software are difficult to compare. Here we present Pathway Signal Flow Calculator (PSFC), a Cytoscape app for calculation of a pathway signal flow based on the pathway topology and node input data. The app provides a rich framework for customization of different signal flow algorithms to allow users to apply various approaches within a single computational framework.
Highlights
Cell signaling pathways are sets of directed interactions between biological molecules, that are initiated by a particular signal and result in realization of certain target processes
Pathway involvement is typically analyzed by overrepresentation analysis (ORA)[1] or gene set enrichment analysis (GSEA)[2]
We present Pathway Signal Flow Calculator (PSFC), a Cytoscape app for computation of pathway signal flow based on input data and pathway topology
Summary
Cell signaling pathways are sets of directed interactions between biological molecules, that are initiated by a particular signal (e.g. a ligand binding to a receptor) and result in realization of certain target processes (e.g. transcription of genes). The above mentioned algorithms and tools are implemented using various programming and scripting languages, making their use and result comparison difficult in the common context They often work with programming environment specific objects, and are not flexible for using biological pathways that appear in various formats. PSFC provides a variety of options for signal propagation, both used in already published signal flow algorithms[3,4,5,6], as well as in new ones. It allows experimenting with the results obtained by various (existing and customizable) approaches within a single framework, and evaluating their ability to simulate real life situations
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