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

TL;DR

DeDaL is a Cytoscape app that creates data-driven biological network layouts from high-throughput molecular data, enabling better visualization of data and network structure for biological insights.

Contribution

It introduces the first method for constructing biological network layouts directly from high-throughput data using dimension reduction algorithms.

Findings

Enables visualization of molecular profiling data on network layouts.

Supports morphing and alignment of network layouts.

Facilitates integrated analysis of network structure and data patterns.

Abstract

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. 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. DeDaL is the first method allowing to construct biological network layouts from high-throughput data. DeDaL is freely available for downloading together with step-by-step tutorial at http://bioinfo-out.curie.fr/projects/dedal/.