xiNET: Cross-link Network Maps With Residue Resolution*

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Abstract

xiNET is a visualization tool for exploring cross-linking/mass spectrometry results. The interactive maps of the cross-link network that it generates are a type of node-link diagram. In these maps xiNET displays: (1) residue resolution positional information including linkage sites and linked peptides; (2) all types of cross-linking reaction product; (3) ambiguous results; and, (4) additional sequence information such as domains. xiNET runs in a browser and exports vector graphics which can be edited in common drawing packages to create publication quality figures. Availability: xiNET is open source, released under the Apache version 2 license. Results can be viewed by uploading data to http://crosslinkviewer.org/ or by downloading the software from http://github.com/colin-combe/crosslink-viewer and running it locally.

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Most cited references 17

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Update on activities at the Universal Protein Resource (UniProt) in 2013

Claire O'Donovan, emmanuel boutet (2012)

The mission of the Universal Protein Resource (UniProt) (http://www.uniprot.org) is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase. It integrates, interprets and standardizes data from numerous resources to achieve the most comprehensive catalogue of protein sequences and functional annotation. UniProt comprises four major components, each optimized for different uses, the UniProt Archive, the UniProt Knowledgebase, the UniProt Reference Clusters and the UniProt Metagenomic and Environmental Sequence Database. UniProt is produced by the UniProt Consortium, which consists of groups from the European Bioinformatics Institute (EBI), the SIB Swiss Institute of Bioinformatics (SIB) and the Protein Information Resource (PIR). UniProt is updated and distributed every 4 weeks and can be accessed online for searches or downloads.

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Topological analysis and interactive visualization of biological networks and protein structures.

Nadezhda T. Doncheva, Yassen Assenov, Francisco S. Domingues … (2012)

Computational analysis and interactive visualization of biological networks and protein structures are common tasks for gaining insight into biological processes. This protocol describes three workflows based on the NetworkAnalyzer and RINalyzer plug-ins for Cytoscape, a popular software platform for networks. NetworkAnalyzer has become a standard Cytoscape tool for comprehensive network topology analysis. In addition, RINalyzer provides methods for exploring residue interaction networks derived from protein structures. The first workflow uses NetworkAnalyzer to perform a topological analysis of biological networks. The second workflow applies RINalyzer to study protein structure and function and to compute network centrality measures. The third workflow combines NetworkAnalyzer and RINalyzer to compare residue networks. The full protocol can be completed in ∼2 h.

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The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

Henning Hermjakob, Luisa Montecchi-Palazzi, Gary Bader … (2004)

A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).

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Author and article information

Journal

Journal ID (nlm-ta): Mol Cell Proteomics

Journal ID (iso-abbrev): Mol. Cell Proteomics

Journal ID (hwp): mcprot

Journal ID (pmc): mcprot

Journal ID (publisher-id): MCP

Title: Molecular & Cellular Proteomics : MCP

Publisher: The American Society for Biochemistry and Molecular Biology

ISSN (Print): 1535-9476

ISSN (Electronic): 1535-9484

Publication date (Print): April 2015

Publication date (Electronic): 3 February 2015

Publication date PMC-release: 3 February 2015

Volume: 14

Issue: 4

Pages: 1137-1147

Affiliations

[1]From the ‡Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom;

[2]§Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany

Author notes

¶ To whom correspondence should be addressed: Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom. Tel.: 44-131-6517056; E-mail: juri.rappsilber@ 123456ed.ac.uk .

Article

Publisher ID: O114.042259

DOI: 10.1074/mcp.O114.042259

PMC ID: 4390258

PubMed ID: 25648531

SO-VID: 1cfb4b39-7305-4313-b58c-2ff98249d5f0

License:

Author's Choice—Final version full access.

History

Date received : 17 June 2014

Date revision received : 19 December 2014

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