Cytoscape space between nodes1/10/2024 There exist numerous methods using biological networks for making insightful high-throughput data analysis. One of the major challenges in systems biology is to combine in a meaningful way the large corpus of molecular biology knowledge recapitulated in the form of large interaction networks together with high-throughput omics data. DeDaL is freely available for downloading at. ConclusionsÄeDaL is a convenient tool for applying data dimensionality reduction methods and for designing insightful data displays based on data-driven layouts of biological networks, built within Cytoscape environment. We demonstrate the added value of applying DeDaL in several practical applications, including an example of a large protein-protein interaction network. The combination of all these functionalities facilitates the creation of insightful network layouts representing both structural network features and correlation patterns in multivariate data. 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. DeDaL is a Cytoscape 3 app, which uses linear and non-linear algorithms of dimension reduction to produce data-driven network layouts based on multidimensional data (typically gene expression). We developed a Cytoscape app, which allows constructing biological network layouts based on the data from molecular profiles imported as values of node attributes. A network layout based simultaneously on the network structure and the associated multidimensional data might be advantageous for data visualization and analysis in some cases. Currently, it is possible to visualize high-throughput data on top of pre-defined network layouts, but they are not always adapted to a given data analysis task. Visualization and analysis of molecular profiling data together with biological networks are able to provide new mechanistic insights into biological functions.
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