Jan 26, 2015

DeDaL: Cytoscape 3.0 app for producing and morphing data-driven and structure-driven network layouts

BioRxiv : the Preprint Server for Biology
Urszula CzerwinskaAndrei Zinovyev

Abstract

Background Visualization and analysis of molecular profiling data together with biological networks are able to provide new mechanistical insights into biological functions. Currently, high-throughput data are usually visualized on top of predefined network layouts which are not always adapted to a given data analysis task. We developed a Cytoscape app which allows to construct biological network layouts based on the data from molecular profiles imported as values of nodes attributes. Results DeDaL is a Cytoscape 3.0 app which uses linear and non-linear algorithms of dimension reduction to produce data-driven network layouts based on multidimensional data (typically gene expression). DeDaL implements several data pre-processing and layout post-processing steps such as continuous morphing between two arbitrary network layouts and aligning one network layout with respect to another one by rotating and mirroring. Combining these possibilities facilitates creating insightful network layouts representing both structural network features and the correlation patterns in multivariate data. Conclusions DeDaL is the first method allowing to construct biological network layouts from high-throughput data. DeDaL is freely available for do...Continue Reading

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Mentioned in this Paper

Patterns
Molecular Profiling
Profile (Lab Procedure)
Gene Expression
APP
Structure
Analysis
Anatomic Node

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