DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes

DisGeNET is a comprehensive discovery platform designed to address a variety of questions concerning the genetic underpinning of human diseases. DisGeNET contains over 380 000 associations between >16 000 genes and 13 000 diseases, which makes it one of the largest repositories currently available of its kind. DisGeNET integrates expert-curated databases with text-mined data, covers information on Mendelian and complex diseases, and includes data from animal disease models. It features a score based on the supporting evidence to prioritize gene-disease associations. It is an open access resource available through a web interface, a Cytoscape plugin and as a Semantic Web resource. The web interface supports user-friendly data exploration and navigation. DisGeNET data can also be analysed via the DisGeNET Cytoscape plugin, and enriched with the annotations of other plugins of this popular network analysis software suite. Finally, the information contained in DisGeNET can be expanded and complemented using Semantic Web technologies and linked to a variety of resources already present in the Linked Data cloud. Hence, DisGeNET offers one of the most comprehensive collections of human gene-disease associations and a valuable set of tools for investigating the molecular mechanisms underlying diseases of genetic origin, designed to fulfill the needs of different user profiles, including bioinformaticians, biologists and health-care practitioners. Database URL: http://www.disgenet.org/

[1]  Henning Hermjakob,et al.  The Reactome pathway Knowledgebase , 2015, Nucleic acids research.

[2]  Takahiro Kawamura,et al.  IMAGE-BASED LITERAL NODE MATCHING FOR LINKED DATA INTEGRATION , 2014 .

[3]  J. Roca,et al.  Network medicine analysis of COPD multimorbidities , 2014, Respiratory Research.

[4]  Núria Queralt-Rosinach,et al.  Extraction of relations between genes and diseases from text and large-scale data analysis: implications for translational research , 2014, BMC Bioinformatics.

[5]  J. Harrow,et al.  Multiple evidence strands suggest that there may be as few as 19 000 human protein-coding genes , 2014, Human molecular genetics.

[6]  Cathy H. Wu,et al.  Activities at the Universal Protein Resource (UniProt) , 2014, Nucleic Acids Research.

[7]  F. Sanz,et al.  A Knowledge-Driven Approach to Extract Disease-Related Biomarkers from the Literature , 2014, BioMed research international.

[8]  Chris T. A. Evelo,et al.  Applying linked data approaches to pharmacology: Architectural decisions and implementation , 2014, Semantic Web.

[9]  Eric J Topol,et al.  Individualized Medicine from Prewomb to Tomb , 2014, Cell.

[10]  Núria Queralt-Rosinach,et al.  The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery , 2014, J. Biomed. Semant..

[11]  Peggy Hall,et al.  The NHGRI GWAS Catalog, a curated resource of SNP-trait associations , 2013, Nucleic Acids Res..

[12]  Masato Kimura,et al.  NCBI’s Database of Genotypes and Phenotypes: dbGaP , 2013, Nucleic Acids Res..

[13]  Judith A. Blake,et al.  The Mouse Genome Database: integration of and access to knowledge about the laboratory mouse , 2013, Nucleic Acids Res..

[14]  María Martín,et al.  Activities at the Universal Protein Resource (UniProt) , 2013, Nucleic Acids Res..

[15]  Damian Smedley,et al.  The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data , 2014, Nucleic Acids Res..

[16]  José Luís Oliveira,et al.  An innovative portal for rare genetic diseases research: The semantic Diseasecard , 2013, J. Biomed. Informatics.

[17]  Doron Lancet,et al.  MalaCards: an integrated compendium for diseases and their annotation , 2013, Database J. Biol. Databases Curation.

[18]  Melinda R. Dwinell,et al.  The Rat Genome Database 2013—data, tools and users , 2013, Briefings Bioinform..

[19]  Thomas C. Wiegers,et al.  The Comparative Toxicogenomics Database: update 2013 , 2012, Nucleic Acids Res..

[20]  Laxmi Parida,et al.  ICT for Bridging Biology and Medicine (Dagstuhl Perspectives Workshop 13342) , 2013, Dagstuhl Manifestos.

[21]  Huajun Chen,et al.  Semantic Web meets Integrative Biology: a survey , 2013, Briefings Bioinform..

[22]  Russ B. Altman,et al.  Introduction to Translational Bioinformatics Collection , 2012, PLoS Comput. Biol..

[23]  Laura Inés Furlong,et al.  The EU-ADR corpus: Annotated drugs, diseases, targets, and their relationships , 2012, J. Biomed. Informatics.

[24]  S. Awasthi,et al.  Association of PPAR‐γ gene polymorphisms with obesity and obesity‐associated phenotypes in north indian population , 2012, American journal of human biology : the official journal of the Human Biology Council.

[25]  Gang Feng,et al.  Disease Ontology: a backbone for disease semantic integration , 2011, Nucleic Acids Res..

[26]  A. Bauer-Mehren,et al.  Gene-Disease Network Analysis Reveals Functional Modules in Mendelian, Complex and Environmental Diseases , 2011, PloS one.

[27]  Lucila Ohno-Machado,et al.  Translational bioinformatics: linking knowledge across biological and clinical realms , 2011, J. Am. Medical Informatics Assoc..

[28]  M. Cawthorne,et al.  Dual acting and pan-PPAR activators as potential anti-diabetic therapies. , 2011, Handbook of experimental pharmacology.

[29]  Laura Inés Furlong,et al.  DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks , 2010, Bioinform..

[30]  Anushya Muruganujan,et al.  PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium , 2009, Nucleic Acids Res..

[31]  M. Feki,et al.  Gender-specific effect of Pro12Ala polymorphism in peroxisome proliferator-activated receptor gamma-2 gene on obesity risk and leptin levels in a Tunisian population. , 2009, Clinical biochemistry.

[32]  I. Ruczinski,et al.  Single nucleotide polymorphisms in obesity-related genes and all-cause and cause-specific mortality: a prospective cohort study , 2009, BMC Medical Genetics.

[33]  A. Compston.  Progressive lenticular degeneration: a familial nervous disease associated with cirrhosis of the liver, by S. A. Kinnier Wilson, (From the National Hospital, and the Laboratory of the National Hospital, Queen Square, London) Brain 1912: 34; 295-509. , 2009, Brain : a journal of neurology.

[34]  Alan F. Scott,et al.  McKusick's Online Mendelian Inheritance in Man (OMIM®) , 2008, Nucleic Acids Res..

[35]  S. Lutsenko.  Atp7b-/- mice as a model for studies of Wilson's disease. , 2008, Biochemical Society transactions.

[36]  Nicole Tourigny,et al.  Bio2RDF: Towards a mashup to build bioinformatics knowledge systems , 2008, J. Biomed. Informatics.

[37]  F. Horber,et al.  The genetic susceptibility to type 2 diabetes may be modulated by obesity status: implications for association studies , 2008, BMC Medical Genetics.

[38]  S. Lutsenko.  Atp 7 b − / − mice as a model for studies of Wilson ’ s disease , 2008 .

[39]  Hans-Peter Kriegel,et al.  Extraction of semantic biomedical relations from text using conditional random fields , 2008, BMC Bioinformatics.

[40]  K. Sirotkin,et al.  The NCBI dbGaP database of genotypes and phenotypes , 2007, Nature Genetics.

[41]  A. Bonvin,et al.  Impaired peroxisome proliferator-activated receptor gamma function through mutation of a conserved salt bridge (R425C) in familial partial lipodystrophy. , 2007, Molecular endocrinology.

[42]  G. Francis,et al.  Peroxisomal proliferator activated receptor-γ deficiency in a Canadian kindred with familial partial lipodystrophy type 3 (FPLD3) , 2006, BMC Medical Genetics.

[43]  T. Buchanan,et al.  Sequence variation in PPARG may underlie differential response to troglitazone. , 2005, Diabetes.

[44]  M. Laakso,et al.  Common polymorphisms of the PPAR-γ2 (Pro12Ala) and PGC-1α (Gly482Ser) genes are associated with the conversion from impaired glucose tolerance to type 2 diabetes in the STOP-NIDDM trial , 2004, Diabetologia.

[45]  N. Campbell.  Genetic association database , 2004, Nature Reviews Genetics.

[46]  Joyce A. Mitchell,et al.  Gene Indexing: Characterization and Analysis of NLM's GeneRIFs , 2003, AMIA.

[47]  Anushya Muruganujan,et al.  PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification , 2003, Nucleic Acids Res..

[48]  J. Berger,et al.  The mechanisms of action of PPARs. , 2002, Annual review of medicine.

[49]  T. Sugiyama,et al.  The Long–Evans Cinnamon rat: An animal model for Wilson’s disease , 1999, Pediatrics international : official journal of the Japan Pediatric Society.

[50]  J. Peppercorn,et al.  The Wilson disease gene is a copper transporting ATPase with homology to the Menkes disease gene , 1993, Nature Genetics.

[51]  H. Chandler.  Database , 1985 .

[52]  S. A. Wilson,et al.  PROGRESSIVE LENTICULAR DEGENERATION: A FAMILIAL NERVOUS DISEASE ASSOCIATED WITH CIRRHOSIS OF THE LIVER , 1912 .

[53]  S. A. Wilson.  PROGRESSIVE LENTICULAR DEGENERATION : A FAMILIAL NERVOUS DISEASE ASSOCIATED WITH CIRRHOSIS OF THE LIVER. , 1912 .