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      Capturing variation impact on molecular interactions in the IMEx Consortium mutations data set

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          Abstract

          The current wealth of genomic variation data identified at nucleotide level presents the challenge of understanding by which mechanisms amino acid variation affects cellular processes. These effects may manifest as distinct phenotypic differences between individuals or result in the development of disease. Physical interactions between molecules are the linking steps underlying most, if not all, cellular processes. Understanding the effects that sequence variation has on a molecule’s interactions is a key step towards connecting mechanistic characterization of nonsynonymous variation to phenotype. We present an open access resource created over 14 years by IMEx database curators, featuring 28,000 annotations describing the effect of small sequence changes on physical protein interactions. We describe how this resource was built, the formats in which the data is provided and offer a descriptive analysis of the data set. The data set is publicly available through the IntAct website and is enhanced with every monthly release.

          Abstract

          Genetic variants might exert their functional effects via influencing molecular interaction. Here, the authors present a resource featuring almost 28,000 annotations describing the effect of small sequence changes on physical protein interactions, curated by IMEx Consortium curators.

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          Most cited references 27

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          Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal.

           J. Gao,  B. Aksoy,  U Dogrusoz (2013)
          The cBioPortal for Cancer Genomics (http://cbioportal.org) provides a Web resource for exploring, visualizing, and analyzing multidimensional cancer genomics data. The portal reduces molecular profiling data from cancer tissues and cell lines into readily understandable genetic, epigenetic, gene expression, and proteomic events. The query interface combined with customized data storage enables researchers to interactively explore genetic alterations across samples, genes, and pathways and, when available in the underlying data, to link these to clinical outcomes. The portal provides graphical summaries of gene-level data from multiple platforms, network visualization and analysis, survival analysis, patient-centric queries, and software programmatic access. The intuitive Web interface of the portal makes complex cancer genomics profiles accessible to researchers and clinicians without requiring bioinformatics expertise, thus facilitating biological discoveries. Here, we provide a practical guide to the analysis and visualization features of the cBioPortal for Cancer Genomics.
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            DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

            The information about the genetic basis of human diseases lies at the heart of precision medicine and drug discovery. However, to realize its full potential to support these goals, several problems, such as fragmentation, heterogeneity, availability and different conceptualization of the data must be overcome. To provide the community with a resource free of these hurdles, we have developed DisGeNET (http://www.disgenet.org), one of the largest available collections of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models and the scientific literature. DisGeNET data are homogeneously annotated with controlled vocabularies and community-driven ontologies. Additionally, several original metrics are provided to assist the prioritization of genotype–phenotype relationships. The information is accessible through a web interface, a Cytoscape App, an RDF SPARQL endpoint, scripts in several programming languages and an R package. DisGeNET is a versatile platform that can be used for different research purposes including the investigation of the molecular underpinnings of specific human diseases and their comorbidities, the analysis of the properties of disease genes, the generation of hypothesis on drug therapeutic action and drug adverse effects, the validation of computationally predicted disease genes and the evaluation of text-mining methods performance.
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              Medical Subject Headings (MeSH).

               John Lipscomb (2000)
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                Author and article information

                Contributors
                pporras@ebi.ac.uk
                Journal
                Nat Commun
                Nat Commun
                Nature Communications
                Nature Publishing Group UK (London )
                2041-1723
                2 January 2019
                2 January 2019
                2019
                : 10
                Affiliations
                [1 ]ISNI 0000 0000 9709 7726, GRID grid.225360.0, European Bioinformatics Institute (EMBL-EBI), , European Molecular Biology Laboratory, ; Wellcome Genome Campus, Hinxton, CB10 1SD UK
                [2 ]ISNI 0000 0001 1515 9979, GRID grid.419481.1, Novartis Institutes for BioMedical Research (NIBR), ; Maulbeerstrasse 66, 4058 Basel, Canton of Basel-Stadt Switzerland
                [3 ]Deep Genomics, MaRS Centre, 661 University Ave, Suite 480, Toronto, ON M5G 1M1 Canada
                [4 ]ISNI 0000 0001 2172 2676, GRID grid.5612.0, Research Programme on Biomedical Informatics (GRIB), Department of Experimental and Health Sciences (DCEXS), Hospital del Mar Medical Research Institute (IMIM), , Universitat Pompeu Fabra (UPF), ; 08003 Barcelona, Spain
                [5 ]Krembil Research Institute, Data Science Discovery Centre for Chronic Diseases, University Health Network, 5KD-407, 60 Leonard Avenue, Toronto, ON M5T 0S8 Canada
                [6 ]ISNI 0000 0001 2157 2938, GRID grid.17063.33, Departments of Medical Biophysics and Computer Science, , University of Toronto, ; Toronto, M4B 1B5 Canada
                [7 ]State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing Institute of Life Omics, 102206 Beijing, China
                [8 ]ISNI 0000 0004 1937 0319, GRID grid.7778.f, DiBEST Department, , University of Calabria, ; Via Pietro Bucci, Rende (CS), 87036 Italy
                [9 ]ISNI 0000 0000 9632 6718, GRID grid.19006.3e, Los Angeles Department of Energy Institute for Genomics and Proteomics, , University of California, ; Los Angeles, CA 90001 USA
                [10 ]ISNI 0000 0001 2300 0941, GRID grid.6530.0, Department of Biology, , University of Rome Tor Vergata, ; Via della Ricerca Scientifica, 00118 Rome, Italy
                [11 ]ISNI 0000 0001 2223 3006, GRID grid.419765.8, Swiss-Prot group, , SIB Swiss Institute of Bioinformatics, ; CMU 1, Rue Michel Servet, 1211 Geneva 4, Switzerland
                [12 ]ISNI 0000 0001 2168 186X, GRID grid.134563.6, School of Animal and Comparative Biomedical Sciences, , University of Arizona, ; Tucson, AZ 85721 USA
                [13 ]ISNI 0000000121901201, GRID grid.83440.3b, Functional Gene Annotation, Institute of Cardiovascular Science, , University College London, ; London, 56273 UK
                [14 ]ISNI 0000 0001 2180 6431, GRID grid.4280.e, Mechanobiology Institute, , National University of Singapore, ; T-Lab #05-01, 5A Engineering Drive 1, Singapore, 117411 Singapore
                [15 ]ISNI 0000 0001 2288 9830, GRID grid.17091.3e, Centre for Microbial Diseases and Immunity Research, , University of British Columbia, ; Lower Mall, Vancouver, 2259 Canada
                [16 ]GRID grid.430453.5, South Australian Health and Medical Research Institute, EMBL Australia Group, ; North Terrace, Adelaide, SA 5001 Australia
                [17 ]ISNI 0000 0004 0367 2697, GRID grid.1014.4, The College of Medicine and Public Health, , Flinders University, ; Bedford Park, SA 5042 Australia
                [18 ]ISNI 0000 0001 2150 7757, GRID grid.7849.2, Univ. Lyon, ICBMS, UMR 5246 CNRS, , Université Lyon 1, ; Villeurbanne Cedex, 69622 Lyon, France
                [19 ]Molecular Connections Pvt. Ltd., Kandala Mansions, 2/2 Kariappa Road, Basavangudi, Bangalore, 560004 India
                Article
                7709
                10.1038/s41467-018-07709-6
                6315030
                30602777
                © The Author(s) 2019

                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/.

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