KeyPathwayMiner

Detects highly-connected sub-networks where most genes show similar expression behavior.
We introduce the latest version of the Key-PathwayMiner software framework. Given a biological network and a set of case- control studies, KeyPathwayMiner efficiently extracts all maximal connected sub-networks. These sub-networks contain the genes that are mainly dysregulated, e.g., differentially expressed, in most cases studied. The exact quantities for “mainly” and “most” are modeled with two easy-to-interpret parameters (K, L) that allows the user to control the number of outliers (not dysregulated genes/cases) in the solutions. We developed two slightly varying models (INES and GLONE) that fall into the class of NP-Hard optimization problems. To tackle the combinatorial explosion of the search space, we designed a set of exact and heuristic algorithms. New features in version 5.0: - Robustness analysis: Test how results vary under different network pertubations and parameter settings - Validation analysis: Upload a gold standard set and test how results vary with different parameter settings.

5.0.1

Works with Cytoscape 3.0

Release Notes

- Bug affecting Mac OSX users was fixed

5.0

Works with Cytoscape 3.0

Release Notes

New features in version 5.0: - Robustness analysis: Test how results vary under different network pertubations and parameter settings - Validation analysis: Upload a gold standard set and test how results vary with different parameter settings.

4.0.2

Works with Cytoscape 3.1

Release Notes

- Fixed compatibility issue with newer versions of Cytoscape (>= 3.1)

4.0.1

Works with Cytoscape 3.0

Release Notes

- Fixed multiple bugs

4.0

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 5.0.1

Released 7 Oct 2016

Works with Cytoscape 3.0

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CYTOSCAPE 2

Version 4.0.2

Released 19 Jul 2013

Works with Cytoscape 2.8

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