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.
Highlights
Biology is a scientific discipline deeply grounded in visual representations serving for communicating results and ideas
We have included in the NaviCell Web Service several methods for graphical representation of molecular data, both broadly used in molecular biology and original ones such as map staining that have not been previously employed in the context of network-based data visualization
We show that NaviCell Web Service can be used for visualization of different types of high-throughput data in two case studies: r comparing two prostate cancer cell lines using the cell cyr cle map, focusing on transcriptomics and mutation data. using the map of molecular interactions involved in Alzheimer’s disease (AD) [19] for visualizing the transcriptome data collected for different brain areas [20]
Summary
Biology is a scientific discipline deeply grounded in visual representations serving for communicating results and ideas. The NaviCell Web Service can exploit pathway maps created by users or from existing databases, including large network maps with thousands of elements. Curie.fr) and other detailed network maps created by research groups for particular topics (Toll-like receptor signalling, EGFR and mTOR pathways, mast cell activation, dendritic cells, iron metabolism, Alzheimer disease and others); (iii) a REST API allowing programmatic use of all data visualization functions and manipulating the web interface.
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