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

Dorel, Mathurin; Viara, Éric; Barillot, Emmanuel; Zinovyev, Andrei; Kuperstein, Inna

doi:10.1093/database/bax026

Cited by 13 publications

(3 citation statements)

References 35 publications

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“…NetGestalt [41] is an advanced tool for integration of multidimensional omics data, exploiting simple and easily readable one-dimensional layouts of gene networks. NaviCom [8] is a novel development that attempts to visualize multi-omics profiles to gain insights into the patterns of regulation of molecular functions. In general, each omics visualization tool has advantages and disadvantages.…”

Section: Characteristics Of the Datamentioning

confidence: 99%

Valorizing omics visualization for discovery

Chichester

2017

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Section: Characteristics Of the Datamentioning

confidence: 99%

Valorizing omics visualization for discovery

Chichester

2017

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“…To facilitate navigation and usage, the map is divided into functional modules. This systems biology resource is freely available, allows easy navigation and curation by the community, facilitated by several web-based platforms such as NaviCell [24], MINERVA [25], and NDEx [26]. Finally, we demonstrate that the RCD map can be used as a tool for comparison of cell death regulation in several human diseases.…”

Section: Introductionmentioning

confidence: 96%

Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases

Ravel

Gómez

Sompairac

et al. 2020

Cancers

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The processes leading to, or avoiding cell death are widely studied, because of their frequent perturbation in various diseases. Cell death occurs in three highly interconnected steps: Initiation, signaling and execution. We used a systems biology approach to gather information about all known modes of regulated cell death (RCD). Based on the experimental data retrieved from literature by manual curation, we graphically depicted the biological processes involved in RCD in the form of a seamless comprehensive signaling network map. The molecular mechanisms of each RCD mode are represented in detail. The RCD network map is divided into 26 functional modules that can be visualized contextually in the whole seamless network, as well as in individual diagrams. The resource is freely available and accessible via several web platforms for map navigation, data integration, and analysis. The RCD network map was employed for interpreting the functional differences in cell death regulation between Alzheimer’s disease and non-small cell lung cancer based on gene expression data that allowed emphasizing the molecular mechanisms underlying the inverse comorbidity between the two pathologies. In addition, the map was used for the analysis of genomic and transcriptomic data from ovarian cancer patients that provided RCD map-based signatures of four distinct tumor subtypes and highlighted the difference in regulations of cell death molecular mechanisms.

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“…NaviCom (https://navicom.curie.fr) is a platform to generate interactive network based molecular portraits using high-throughput datasets. Additionally, NaviCom connects with the cBioPortal database (www.cbioportal.org) (Cerami et al, 2014) and NaviCell web service, and it allows to display various high-throughput data types simultaneously on the network maps in a user-friendly way (Dorel et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Atlas of Cancer Signaling Network: A Resource of Multi-Scale Biological Maps to Study Disease Mechanisms

et al. 2021

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ACSN (https://acsn.curie.fr) is a web-based resource of multi-scale biological maps depicting molecular processes in cancer cell and tumor microenvironment. The core of the Atlas is a set of interconnected cancer-related signaling and metabolic network maps. Molecular mechanisms are depicted on the maps at the level of biochemical interactions, forming a large seamless network. The Atlas is a "geographic-like" interactive "world map" of molecular interactions leading the hallmarks of cancer as described by Hanahan and Weinberg. The Atlas is created using the systems biology standards and therefore is amenable for computational analysis. The maps of ACSN are organized in a hierarchical manner and decomposed into functional modules with meaningful network layout. Navigation of the ACSN is intuitive thanks to the Google Maps-like features in the NaviCell web platform. Particularly, the exploration of the Atlas is simplified due to the semantic zooming feature, allowing the user to visualize the seamless Atlas and individual maps from the collection at different levels of details. The resource includes tools for visualization and analysis of molecular data in the context of signaling network maps. In this chapter we present how a disease-specific resource such as the Atlas of Cancer Signaling Network (ACSN) can be useful to study and interpret molecular perturbations in cancer, among others, explaining drug resistance, suggesting intervention points, finding phenotype shifts through disease progression, explaining susceptibility to a particular type of cancer and studying disease comorbidities.

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

Cited by 13 publications

References 35 publications

Valorizing omics visualization for discovery

Valorizing omics visualization for discovery

Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases

Atlas of Cancer Signaling Network: A Resource of Multi-Scale Biological Maps to Study Disease Mechanisms

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