  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/.
