Metascape provides a biologist-oriented resource for the analysis of systems-level datasets

Abstract

A critical component in the interpretation of systems-level studies is the inference of enriched biological pathways and protein complexes contained within OMICs datasets. Successful analysis requires the integration of a broad set of current biological databases and the application of a robust analytical pipeline to produce readily interpretable results. Metascape is a web-based portal designed to provide a comprehensive gene list annotation and analysis resource for experimental biologists. In terms of design features, Metascape combines functional enrichment, interactome analysis, gene annotation, and membership search to leverage over 40 independent knowledgebases within one integrated portal. Additionally, it facilitates comparative analyses of datasets across multiple independent and orthogonal experiments. Metascape provides a significantly simplified user experience through a one-click Express Analysis interface to generate interpretable outputs. Taken together, Metascape is an effective and efficient tool for experimental biologists to comprehensively analyze and interpret OMICs-based studies in the big data era.

Abstract

With the increasing obtainability of multi-OMICs data comes the need for easy to use data analysis tools. Here, the authors introduce Metascape, a biologist-oriented portal that provides a gene list annotation, enrichment and interactome resource and enables integrated analysis of multi-OMICs datasets.

Contributors

Yingyao Zhou: [e-mail]

Sumit K. Chanda: [e-mail]

Journal

Journal ID (nlm-ta): Nat Commun

Journal ID (iso-abbrev): Nat Commun

Title: Nature Communications

Publisher: Nature Publishing Group UK (London )

ISSN (Electronic): 2041-1723

Publication date (Electronic): 3 April 2019

Publication date PMC-release: 3 April 2019

Publication date Collection: 2019

Volume: 10

Affiliations

[1 ]ISNI 0000 0004 0627 6737, GRID grid.418185.1, Genomics Institute of the Novartis Research Foundation, ; 10675 John Jay Hopkins Drive, San Diego, CA 92121 USA

[2 ]ISNI 0000 0001 0163 8573, GRID grid.479509.6, Immunity and Pathogenesis Program, Infectious and Inflammatory Disease Center, , Sanford Burnham Prebys Medical Discovery Institute, ; 10901 North Torrey Pines Road, La Jolla, CA 92037 USA

[3 ]ISNI 0000 0001 2107 4242, GRID grid.266100.3, Department of Medicine, , University of California, San Diego, ; 9500 Gilman Drive, La Jolla, CA 92093 USA

Article

Publisher ID: 9234

DOI: 10.1038/s41467-019-09234-6

PMC ID: 6447622

PubMed ID: 30944313

Copyright statement: © The Author(s) 2019

License:

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

Categories

Subject: Article

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issue-copyright-statement © The Author(s) 2019