PSFC

Pathway Signal Flow Calculator: Calculates pathway activity based on gene expression/metabolite abundance and pathway topology.
Pathway activity is estimated by its capacity to propagate an amount of signal from the input to the outputs. PSFC estimates the signal flow propagation on pathways based on the pathway topology and node input data. With PSFC you can: * Calculate the signal flow propagation based on gene expression, gene methylation, protein activity, and any other type of data. * Estimate the activity state of the pathway and its component nodes: compare these states in health and disease. * Apply custom algorithms to model signal propagation on the pathway. * Visualize flow propagation in Cytoscape. We have opened a PSFC discussion group at https://groups.google.com/forum/#!forum/psfc-discussion-group. Please, post your questions and comments to the group, or e-mail your quesionts and thoughts. Citation: Nersisyan L, Johnson G, Riel-Mehan M et al. PSFC: a Pathway Signal Flow Calculator App for Cytoscape [v1; ref status: awaiting peer review, http://f1000r.es/5k3] F1000Research 2015, 4:480 (doi: [http://f1000research.com/articles/4-480/v1 10.12688/f1000research.6706.1])

1.1.2

Works with Cytoscape 3.4

Release Notes

### What’s new in 1.1.2 (compared to 1.0.2): *Major points:* **Run PSF for multiple columns** In 1.1.2, the user is able to simultaneously select multiple columns containing node data from multiple samples to run PSF on all of them in succession, as opposed to performing many PSF computations manually. **Operator nodes** In version 1.1.2, the user may specify signal transfer functions not only on edges, but also on specific nodes. In this way, each node may appear as in ‘operator’ that takes input signals from multiple incoming edges and processes them in a unique way. This is particularly useful for: - Protein complexes: usually the presence of all the complex subunits is mandatory for it to function. In this case the user may set the ‘min’ function onto the complex node. This means that the subunit with the minimum abundance will be the limiting factor for the activity of the whole complex. - Many proteins/complexes compensating each other’s functions. In situations when the presence of either protein/complex is enough for the signal to transduce, the user may create an ‘operator’ node and assign the ‘max’ function to it. - Sometimes, the ‘mean’ (average signal) and the ‘prod’ (product of signal multiplications) is desirable, if the user is interested in general state of the summary states of input signals. *Minor points:* - PSF visualization is now fully customizable, with the option to set the minimum and maximum SPFs to the desired value. - Many bug fixes.

1.0.2

Works with Cytoscape 3.0

Release Notes

Visualization is adjusted for custom-set two color scheme and custom edge width ranges. The play flow button is removed, so the user can control the visualization with their desired pace. User Manual updated.

1.0.1

Works with Cytoscape 3.0

Release Notes

Bug fixed: unable to map node scores to Cytoscape attribute. Minor changes: loop handling - corrected number of iterations; bootstrap calculations - validation of the user supplied number of samplings (to be numberic); "split.incoming: and "addition" rules set as default; min width of edges changed

1.0.0

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 1.1.2

Released 28 Mar 2017

Works with Cytoscape 3.4

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