cyTransFinder

Signal Transduction Pathway Finder
### About CyTRANSFINDER is a new Cytoscape 3.x plugin that supports the reconstruction of small signal transduction pathways among groups of genes. Signal Transduction Pathways are molecular circuits that model how cells receive, process, and respond to information from the environment providing snapshots of the overall cell dynamics. Most of the attempts to reconstruct signal transaction pathways are limited to single regulator networks including gene/protein. However, networks involving a single type of regulator and neglecting post-transcriptional regulation mediated by miRNAs interacting with different transcription factors may not fully reveal the complex regulatory mechanisms of a cell. We have developed CyTRANSFINDER, to enable users to infer three-component signal transduction pathways with the presence of miRNAs, TFs and genes based on user defined regulatory patterns. CyTRANSFINDER has been designed to support exploratory analysis, it therefore does not rely on expression data. ### CyTransFinder at a glance Labels in this section are referred to the screenshot. + (A) The main plug-in control panel. It allows the user to set the source and destination list of genes and the specific pattern of regulators to search. + (B) Shows the graphical output of the plugin that consists of a network connecting source genes with destination genes. Nodes of this network represent genes, TFs and miRNAs. + (C) This pane allows to define a set of parameters related to the integration of miRNAs into the generated STPs. They can be used to control the size of the generated networks. + (D) This pane allows the user to export the results in the form of a text file including all identified circuits or to delete the current experiment and start with a new one. + (E) The Cytosdcape node and edge tables. They can be used to access detailed information on the nodes and arcs of the identified STPs. ### Code Availability The full CyTransFinder code is available in the [repository (click here)](http://cytoscape.org)

1.71

Works with Cytoscape 3.3

API   pom.xml   Javadocs

Release Notes

Update: some online services have changed their interface commands and output format. The plugin has been updated accordingly.

1.6

Works with Cytoscape 3.3

API   pom.xml   Javadocs

Release Notes

Update! After few days of problems everything sounds ok now!! Changes: updated the URL of two repositories

1.5

Works with Cytoscape 3.3

API   pom.xml   Javadocs

Release Notes

Bug Fixes and optimisation

1.4

Works with Cytoscape 3.3

API   pom.xml   Javadocs

Release Notes

BugFixes

1.3

Works with Cytoscape 3.3

API   pom.xml   Javadocs

Release Notes

Improvements for higher performance on STPs analysis

1.2

Works with Cytoscape 3.3

API   pom.xml   Javadocs

Release Notes

**BugFixes and Enhancements** - Upgraded the whole set of libraries to the last Cytoscape_3.4.0_SNAPSHOT - Minor updates to enhance plugin reliability and execution speed **NewFeatures** 1) Input files (source and target lists) may be defined as a comma separated list of + Gene ID + Gene Symbol + GeneID,GeneSymbol + microRNAs annotated as hsa-mir-xxx (this option is only valid for the source file) 2) Two new predefined STPs available (they work with microRNAs as source entities): + Indirect s. miRNA - composed by the following entities: sourcemirna,tf,targetgene + Double s. miRNA indirect - composed by the following entities: sourcemirna,tf,gene,imirna,targetgene 3) Provided a STTP Type help link in the GUI, which describes the STPs predefined in the plugin 4) Added a control windows that confirm to the user the results obtained after the run 5) The NODETABLE now contains links to NCBI/Mirbase pages related to any entity included in the STPs found

1.1

Works with Cytoscape 3.0


1

Works with Cytoscape 3.0


CYTOSCAPE 3

Version 1.71

License Click here

Released 16 Mar 2017

Works with Cytoscape 3.3

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