ENViz

Enrichment analysis and visualization - integrated analysis of multiple sample matched data sets in the context of systematic annotation
**ENViz** is an ENrichment analysis and VisualiZation plugin for integrated analysis of multiple sample matched data sets in the context of systematic annotation. ENViz analyses a primary data set (e.g. gene expression) with respect to a pivot data set (e.g. miRNA expression, other non-coding RNA expression or proteomics measurements) and to primary data annotation (e.g. pathway or gene ontology) in the following way. For each pivot entry, we rank elements of the primary data based on the correlation to the pivot across all samples, and compute statistical enrichment of annotation elements at the top of this ranked list based on the minimum hypergeometric statistics (Eden et al, 2007, Eden et al, 2009). Significant results are represented as an enrichment network - a bipartite graph with nodes corresponding to pivot and annotation entries, and edges corresponding to pivot-annotation entry pairs with enrichment scores above the user defined threshold. Correlations of primary data and pivot data can be visually overlaid on biological pathways for significant pivot-annotation pairs using WikiPathways resource (Kelder et al, 2012). In the context of gene ontology (GO), enrichment network can be overlaid on top of GO hierarchy. Edges of the enrichment network point to potential functionally relevant mechanisms. "ENViz: A Cytoscape App for Integrated Statistical Analysis and Visualization of Sample-Matched Data with Multiple Data Types." *Steinfeld I, Navon R, Creech ML, Yakhini Z, Tsalenko A*, Bioinformatics, Jan 2015, PMID: 25577435.

3.1.5

Works with Cytoscape 3.2

Release Notes

This is a bug fix release that requires running with WikiPathways 3.2.1+ and Cytoscape 3.2.0+ (it is unknown if newer versions of Cytoscape work with this plugin). Following are the updates for this release: 1. Fixed bug where displaying WikiPathways would always fail due to change in WikiPathways API and a WikiPathways bug. 2. Changed to use WikiPathways 3.2.1.

3.1.4

Works with Cytoscape 3.1

Apps that depend on this release

Release Notes

This is a bug fix release with the following updates: <OL> <LI>Changed ENViz to sidestep threading bugs in other Cytoscape components, such as the Browser, that display as ArrayIndexOutOfBoundsExceptions during the visualization of pathways. <LI>Changed to use WikiPathways 3.2.0. <LI>Updated WikiPathway flatfiles used by ENViz to 12/16/14. <LI>Fixed initial task message to not say 'Copying Data Files from ENViz null'. </OL>

3.1.3

Works with Cytoscape 3.1

Release Notes

A bug release with the following changes: <OL> <LI>Changed download of stale or missing GO data files to specify where the files are being downloaded from. <LI>Fixed incorrect error message when a local GO .obo file has never been downloaded and you attempt to visualize a GO results file when not connected to the Internet. <LI>Updated to use WikiPathways 3.1.2 (required for Cy 3.2.0). <BR><B>Important: Make sure WikiPathways 3.1.2, or later, is installed and remove WikiPathways 3.1.1.</B> <LI>Updated WikiPathway flatfiles used by ENViz to 11/17/14. <LI>Changed feedback message while loading pathways for a pivot node to include the pivot node's name. </OL> Known problems in this release: <OL> <LI>If you install ENViz in a running Cytoscape, you will need to exit and rerun Cytoscape before ENViz will show up. <BR>This will be fixed after Cytoscape 3.2.1 is released. </OL>

3.1.2

Works with Cytoscape 3.1

Release Notes

A bug fix release with the following changes: <OL> <LI>Fixed bug where coloring of wikipathways was not happening in certain cases. <LI>Changed wikiPathway label coloring so that there aren't cases where we have unreadable labels. <LI>Updated help tutorial (10/20/14). <LI>Fixed unclear error message about missing wikiPathways visual style to mention possibly being off-line. <LI>Updated WikiPathway flatfiles used by ENViz to (10/16/14). </OL> Known problems in this release: <OL> <LI>If you install ENViz in a running Cytoscape, you will need to exit and rerun Cytoscape before ENViz will show up. <BR>This will be fixed after Cytoscape 3.1.2 is released. </OL>

3.1.1

Works with Cytoscape 3.1

Release Notes

This version requires Cy 3.1+, or later. For general info on installing, running, and configuring ENViz, see the <a href="http://bioinfo.cs.technion.ac.il/people/zohar/ENViz/Cy3-README-user.pdf">ENViz User README</a>. Specific changes in this release include: <OL> <LI>Clunky window flashing has been removed when wikipathway networks are created and displayed. <LI>Added False Discovery Rate (FDR) as attribute to each enrichment network. <BR>FDR is calculated as <em>(expected number of significant edges)/(observed number of significant edges)</em>. Where <em>observed number of significant edges</em> is the number of edges in enrichment network with enrichment scores above Enrichment Display Cutoff. And <em>expected number of edges</em> is: <pre> (number of annotation categories)x(number of pivots)x10^(-Enrichment Display Cutoff) </pre> <LI>Changed visual style of GO and Pathway enrichment networks to have bold, 12pt, Helvetica font with single pixel dark gray borders, increased pathway node size. <LI>Changed pathway visual style node label transparency to range from 125 - 255 (was 75 - 255). <LI>Changed 'EnrichmentCorrelation' attribute to 'Correlation'. <LI>Changed timing feedback presented during Analysis to be more concise. <BR>Changed the order of timing info to have remaining time first and changed to use abbreviations for hours, minutes, and seconds. <LI>Fixed bug where pivot and GO networks were not colored correctly. <BR>This was caused by equation for EnrichmentValue not correctly matching the VA being used. <LI>Fixed bug where a failed visualization of an analysis results file, caused by too high a cutoff, stops spectrum modeling from running on a future visualization of the analysis results file. <LI>Fixed parsing bug where an IllegalArgumentException would occur when reading new GO hierarchy data from the geneontology.org website. <BR>New Stanza types were added to the gene_ontology_edit.obo file and ENViz needed to skip tag-value pairs found within them. <LI>Fixed bug where long GO node labels whould go way outside node box. <LI>Fixed bug where no feedback would be shown during analysis. <LI>Fixed potential deadlock bug where modal Cytoscape TaskMonitor dialog could deadlock with ENViz modal dialog messages by adding a non-modal ENViz dialog. <LI>Fixed to run with new application home directory determined by Cytoscape (based on Cytoscape fix to Redmine bug 2162). <BR>When a new version of ENViz is initially run only older versions of ENViz that use this home directory change will be found for copying property files from the older version of ENViz to the newer version. <LI>When moving between versions of ENViz, GO data files will now be copied along with ENViz property files. <BR>Only GO files that are not stale are copied. The copy process can be halted by clicking on the 'X' in the middle of the task monitor dialog. <LI>Fixed ENViz to visualize old analysis files that have incorrect GO data or missing "B" data. <BR>Edge statistics are set to "-1" for bad data entries. <LI>Fixed IllegalArgumentException when newly created CyNetwork's are destroyed due to an error. <LI>Fixed bug where a failed visualization of an analysis results file, caused by too high a cutoff, stops spectrum modeling from running on a future visualization of the analysis results file. <LI>Fixed sliders to better handle poor data that would have the lower bound and upper bounds sliders overlap. <BR>Also attempts to fix bad slider data read in from the archive (e.g., low value > high value). <LI>Improved error messages to separate user data input errors from analysis failure due to some bug. <LI>Stopped ugly, red error temporary equation error values in Table Panel Node Table for NormalizedCumEnrichmentValue. <LI>Slight modifications to Agilent ENViz Control Panel Tab sizing to helpe minimize need for scrollbars. <LI>Wikipathways is no longer loaded as part of ENViz and ENViz now uses WikiPathways v3.1.1+. <LI>Changed ENViz to be a bundle plugin. </OL> Known problems in this release: <OL> <LI>Saving and restoring a session containing pathway enrichment networks will not have the pathways correctly colored (due to a Cytoscape bug with session restore of equations). <LI>Some dialogs are not centered within the Cytoscape window correctly. </OL>

CYTOSCAPE 3

Version 3.1.5

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Released 9 Oct 2017

Works with Cytoscape 3.2

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CYTOSCAPE 2

Version 1.1

Released 29 Apr 2014

Works with Cytoscape 2.8

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