title: NaviCell Web Service for network-based data visualization.
abstract: Data visualization is an essential element of biological research, required for obtaining insights and formulating new hypotheses on mechanisms of health and disease. NaviCell Web Service is a tool for network-based visualization of 'omics' data which implements several data visual representation methods and utilities for combining them together. NaviCell Web Service uses Google Maps and semantic zooming to browse large biological network maps, represented in various formats, together with different types of the molecular data mapped on top of them. For achieving this, the tool provides standard heatmaps, barplots and glyphs as well as the novel map staining technique for grasping large-scale trends in numerical values (such as whole transcriptome) projected onto a pathway map. The web service provides a server mode, which allows automating visualization tasks and retrieving data from maps via RESTful (standard HTTP) calls. Bindings to different programming languages are provided (Python and R). We illustrate the purpose of the tool with several case studies using pathway maps created by different research groups, in which data visualization provides new insights into molecular mechanisms involved in systemic diseases such as cancer and neurodegenerative diseases.
authors.affiliation: Institut Curie, 26 rue d'Ulm, 75248 Paris, France INSERM, U900, 75248 Paris, France Mines ParisTech, 77300 Fontainebleau, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Bonnet
authors.affiliation: Sysra, 91330 Yerres, France.
authors.forename: Eric
authors.initials: E
authors.lastname: Viara
authors.affiliation: Institut Curie, 26 rue d'Ulm, 75248 Paris, France INSERM, U900, 75248 Paris, France Mines ParisTech, 77300 Fontainebleau, France.
authors.forename: Inna
authors.initials: I
authors.lastname: Kuperstein
authors.affiliation: Institut Curie, 26 rue d'Ulm, 75248 Paris, France INSERM, U900, 75248 Paris, France Mines ParisTech, 77300 Fontainebleau, France.
authors.forename: Laurence
authors.initials: L
authors.lastname: Calzone
authors.affiliation: Institut Curie, 26 rue d'Ulm, 75248 Paris, France INSERM, U900, 75248 Paris, France Mines ParisTech, 77300 Fontainebleau, France.
authors.forename: David P A
authors.initials: DP
authors.lastname: Cohen
authors.affiliation: Institut Curie, 26 rue d'Ulm, 75248 Paris, France INSERM, U900, 75248 Paris, France Mines ParisTech, 77300 Fontainebleau, France.
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Barillot
authors.affiliation: Institut Curie, 26 rue d'Ulm, 75248 Paris, France INSERM, U900, 75248 Paris, France Mines ParisTech, 77300 Fontainebleau, France andrei.zinovyev@curie.fr.
authors.forename: Andrei
authors.initials: A
authors.lastname: Zinovyev
mesh_terms: D000465:Algorithms; D000544:Alzheimer Disease / Q000235:genetics; D001921:Brain / Q000378:metabolism; D045744:Cell Line, Tumor; D003196:Computer Graphics; D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D008297:Male; D009154:Mutation; D011471:Prostatic Neoplasms / Q000235:genetics; D012984:Software