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Version 2. F1000Res. 2015 Aug 5 [revised 2017 Apr 3];4:480. doi: 10.12688/f1000research.6706.2. eCollection 2015.

PSFC: a Pathway Signal Flow Calculator App for Cytoscape.

Author information

1
Institute of Molecular Biology NAS RA, Yerevan, Armenia.
2
University of California, San Francisco, CA, 94158, USA.
3
California Institute for Quantitative Biosciences (QB3), San Francisco, CA, 94158, USA.
4
Gladstone Institutes, San Francisco, CA, 94158, USA.
5
American University of Armenia, Yerevan, Armenia.

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.

KEYWORDS:

cytoscape; gene expression; networks; pathway signal flow; scoring algorithms; systems biology

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