NaviCom: a web application to create interactive molecular network portraits using multi-level omics data.

Mathurin Dorel,Eric Viara,Inna Kuperstein,Andrei Zinovyev,Emmanuel Barillot

doi:10.1093/database/bax026

Mathurin Dorel, Eric Viara + Show 3 more

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https://doi.org/10.1093/database/bax026

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Abstract

Human diseases such as cancer are routinely characterized by high-throughput molecular technologies, and multi-level omics data are accumulated in public databases at increasing rate. Retrieval and visualization of these data in the context of molecular network maps can provide insights into the pattern of regulation of molecular functions reflected by an omics profile. In order to make this task easy, we developed NaviCom, a Python package and web platform for visualization of multi-level omics data on top of biological network maps. NaviCom is bridging the gap between cBioPortal, the most used resource of large-scale cancer omics data and NaviCell, a data visualization web service that contains several molecular network map collections. NaviCom proposes several standardized modes of data display on top of molecular network maps, allowing addressing specific biological questions. We illustrate how users can easily create interactive network-based cancer molecular portraits via NaviCom web interface using the maps of Atlas of Cancer Signalling Network (ACSN) and other maps. Analysis of these molecular portraits can help in formulating a scientific hypothesis on the molecular mechanisms deregulated in the studied disease. Database URL: NaviCom is available at https://navicom.curie.fr

Highlights

Today’s biology is largely data-driven, thanks to highthroughput technologies that allow investigating molecular and cellular aspects of life at large scale
To highlight the possibilities provided by this tool, we demonstrate how multi-level cancer omics data from cBioPortal [3] are automatically visualized on the molecular network maps available in Atlas of Cancer Signalling Network (ACSN) [13] and NaviCell [24] collections
We show how NaviCom solves the problem of connecting the omics data resource cBioPortal and the collection of signalling maps in ACSN and NaviCell; and optimizes data visualization

Summary

Introduction

Today’s biology is largely data-driven, thanks to highthroughput technologies that allow investigating molecular and cellular aspects of life at large scale These technologies comprise microarray platforms, next-generation sequencers, mass spectrometers, or interaction screens, producing multi-level omics data such as gene and protein expression, mutational profiles, epigenetic landscapes, etc [1, 2]. A lot of information about molecular mechanisms is available in the scientific literature, and is integrated into signalling pathway databases Those signalling pathway databases, such as Reactome [7], KEGG PATHWAYS [8], Spike [9], PathwaysCommons [10], ConsensusPathDB [11], SIGNOR [12], Atlas of Cancer Signalling Network (ACSN) [13] etc, vary in the approach to depict molecular interactions and in the level of details of biological processes representation [14]. Some pathway databases contain integrated data visualization tools such as the Reactome Analysis tools or FuncTree for KEGG PATHWAYS [22]

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