The Comparative Toxicogenomics Database: update 2013
Allan Peter Davis,Cynthia G. Murphy,Robin J. Johnson,Jean M. Lay,Kelley Lennon-Hopkins,Cynthia A. Saraceni-Richards,Daniela Sciaky,Benjamin L. King,Michael C. Rosenstein,Thomas C. Wiegers,Carolyn J. Mattingly +10 more
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TLDR
The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between environmental chemicals and gene products and their relationships to diseases as discussed by the authors, which can help users generate testable hypotheses about the molecular mechanisms of environmental diseases.Abstract:
The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between environmental chemicals and gene products and their relationships to diseases. Chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature are integrated to generate expanded networks and predict many novel associations between different data types. CTD now contains over 15 million toxicogenomic relationships. To navigate this sea of data, we added several new features, including DiseaseComps (which finds comparable diseases that share toxicogenomic profiles), statistical scoring for inferred gene-disease and pathway-chemical relationships, filtering options for several tools to refine user analysis and our new Gene Set Enricher (which provides biological annotations that are enriched for gene sets). To improve data visualization, we added a Cytoscape Web view to our ChemComps feature, included color-coded interactions and created a 'slim list' for our MEDIC disease vocabulary (allowing diseases to be grouped for meta-analysis, visualization and better data management). CTD continues to promote interoperability with external databases by providing content and cross-links to their sites. Together, this wealth of expanded chemical-gene-disease data, combined with novel ways to analyze and view content, continues to help users generate testable hypotheses about the molecular mechanisms of environmental diseases.read more
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A circadian gene expression atlas in mammals: Implications for biology and medicine
TL;DR: High-resolution multiorgan expression data is generated showing that nearly half of all genes in the mouse genome oscillate with circadian rhythm somewhere in the body, and the majority of best-selling drugs and World Health Organization essential medicines directly target the products of rhythmic genes.
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The support of human genetic evidence for approved drug indications
Matthew R. Nelson,Hannah Tipney,Jeffery L. Painter,Judong Shen,Paola Nicoletti,Yufeng Shen,Aris Floratos,Pak C. Sham,Mulin Jun Li,Junwen Wang,Lon R. Cardon,John C. Whittaker,Philippe Sanseau +12 more
TL;DR: It is estimated that selecting genetically supported targets could double the success rate in clinical development, and using the growing wealth of human genetic data to select the best targets and indications should have a measurable impact on the successful development of new drugs.
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DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes
Janet Piñero,Núria Queralt-Rosinach,Àlex Bravo,Jordi Deu-Pons,Anna Bauer-Mehren,Martin Baron,Ferran Sanz,Laura I. Furlong +7 more
TL;DR: 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, are offered.
Journal ArticleDOI
Understanding multicellular function and disease with human tissue-specific networks
Casey S. Greene,Arjun Krishnan,Aaron K. Wong,Emanuela Ricciotti,Rene A. Zelaya,Daniel Himmelstein,Ran Zhang,Boris M. Hartmann,Elena Zaslavsky,Stuart C. Sealfon,Daniel I. Chasman,Garret A. FitzGerald,Kara Dolinski,Tilo Grosser,Olga G. Troyanskaya +14 more
TL;DR: NetWAS is introduced, which combines genes with nominally significant genome-wide association study (GWAS) P values and tissue-specific networks to identify disease-gene associations more accurately than GWAS alone.
Journal ArticleDOI
The Comparative Toxicogenomics Database: update 2019.
Allan Peter Davis,Cynthia J. Grondin,Robin J. Johnson,Daniela Sciaky,Roy McMorran,Jolene Wiegers,Thomas C. Wiegers,Carolyn J. Mattingly +7 more
TL;DR: This biennial update presents a new chemical–phenotype module that codes chemical-induced effects on phenotypes, curated using controlled vocabularies for chemicals, phenotype, taxa, and anatomical descriptors, and describes new querying and display features for the enhanced chemical–exposure science module, providing greater scope of content and utility.
References
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Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
Journal ArticleDOI
Database resources of the National Center for Biotechnology Information
David L. Wheeler,Deanna M. Church,Ron Edgar,Scott Federhen,Wolfgang Helmberg,Thomas L. Madden,Joan Pontius,Gregory D. Schuler,Lynn M. Schriml,Edwin Sequeira,Tugba O. Suzek,Tatiana Tatusova,Lukas Wagner +12 more
TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
Journal ArticleDOI
KEGG for integration and interpretation of large-scale molecular data sets
TL;DR: KEGG Mapper, a collection of tools for KEGG PATHWAY, BRITE and MODULE mapping, enabling integration and interpretation of large-scale data sets and recent enhancements to the K EGG content, especially the incorporation of disease and drug information used in practice and in society, to support translational bioinformatics.
Journal ArticleDOI
Reactome: a database of reactions, pathways and biological processes
David Croft,Gavin O'Kelly,Guanming Wu,Robin Haw,Marc Gillespie,Lisa Matthews,Michael Caudy,Phani V. Garapati,Gopal R. Gopinath,Bijay Jassal,S Jupe,Irina Kalatskaya,Shahana S. Mahajan,Shahana S. Mahajan,Bruce May,Nelson Ndegwa,Esther Schmidt,Veronica Shamovsky,Christina K. Yung,Ewan Birney,Henning Hermjakob,Peter D'Eustachio,Lincoln Stein,Lincoln Stein,Lincoln Stein +24 more
TL;DR: A new web site with improved tools for pathway browsing and data analysis is developed, and orthology-based inferences of pathways in non-human species are made, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species.
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