- T1DBase: update 2011, organization and presentation of large-scale data sets for type 1 diabetes research. [PMID: 20937630]
Oliver S Burren, Ellen C Adlem, Premanand Achuthan, Mikkel Christensen, Richard M R Coulson, John A Todd
Nucleic acids research 2011:39(Database issue)
56 Citations (Google Scholar as of 2016-05-08)
Abstract: T1DBase (http://www.t1dbase.org) is web platform, which supports the type 1 diabetes (T1D) community. It integrates genetic, genomic and expression data relevant to T1D research across mouse, rat and human and presents this to the user as a set of web pages and tools. This update describes the incorporation of new data sets, tools and curation efforts as well as a new website design to simplify site use. New data sets include curated summary data from four genome-wide association studies relevant to T1D, HaemAtlas-a data set and tool to query gene expression levels in haematopoietic cells and a manually curated table of human T1D susceptibility loci, incorporating genetic overlap with other related diseases. These developments will continue to support T1D research and allow easy access to large and complex T1D relevant data sets.
- T1DBase: integration and presentation of complex data for type 1 diabetes research. [PMID: 17169983]
Erin M Hulbert, Luc J Smink, Ellen C Adlem, James E Allen, David B Burdick, Oliver S Burren, Victor M Cassen, Christopher C Cavnor, Geoffrey E Dolman, Daisy Flamez, Karen F Friery, Barry C Healy, Sarah A Killcoyne, Burak Kutlu, Helen Schuilenburg, Neil M Walker, Josyf Mychaleckyj, Decio L Eizirik, Linda S Wicker, John A Todd, Nathan Goodman
Nucleic acids research 2007:35(Database issue)
77 Citations (Google Scholar as of 2016-05-08)
Abstract: T1DBase (http://T1DBase.org) [Smink et al. (2005) Nucleic Acids Res., 33, D544-D549; Burren et al. (2004) Hum. Genomics, 1, 98-109] is a public website and database that supports the type 1 diabetes (T1D) research community. T1DBase provides a consolidated T1D-oriented view of the complex data world that now confronts medical researchers and enables scientists to navigate from information they know to information that is new to them. Overview pages for genes and markers summarize information for these elements. The Gene Dossier summarizes information for a list of genes. GBrowse [Stein et al. (2002) Genome Res., 10, 1599-1610] displays genes and other features in their genomic context, and Cytoscape [Shannon et al. (2003) Genome Res., 13, 2498-2504] shows genes in the context of interacting proteins and genes. The Beta Cell Gene Atlas shows gene expression in beta cells, islets, and related cell types and lines, and the Tissue Expression Viewer shows expression across other tissues. The Microarray Viewer shows expression from more than 20 array experiments. The Beta Cell Gene Expression Bank contains manually curated gene and pathway annotations for genes expressed in beta cells. T1DMart is a query tool for markers and genotypes. PosterPages are 'home pages' about specific topics or datasets. The key challenge, now and in the future, is to provide powerful informatics capabilities to T1D scientists in a form they can use to enhance their research.
- T1DBase, a community web-based resource for type 1 diabetes research. [PMID: 15608258]
Luc J Smink, Erin M Helton, Barry C Healy, Christopher C Cavnor, Alex C Lam, Daisy Flamez, Oliver S Burren, Yang Wang, Geoffrey E Dolman, David B Burdick, Vincent H Everett, Gustavo Glusman, Davide Laneri, Lee Rowen, Helen Schuilenburg, Neil M Walker, Josyf Mychaleckyj, Linda S Wicker, Decio L Eizirik, John A Todd, Nathan Goodman
Nucleic acids research 2005:33(Database issue)
45 Citations (Google Scholar as of 2016-05-08)
Abstract: T1DBase (http://T1DBase.org) is a public website and database that supports the type 1 diabetes (T1D) research community. The site is currently focused on the molecular genetics and biology of T1D susceptibility and pathogenesis. It includes the following datasets: annotated genome sequence for human, rat and mouse; information on genetically identified T1D susceptibility regions in human, rat and mouse, and genetic linkage and association studies pertaining to T1D; descriptions of NOD mouse congenic strains; the Beta Cell Gene Expression Bank, which reports expression levels of genes in beta cells under various conditions, and annotations of gene function in beta cells; data on gene expression in a variety of tissues and organs; and biological pathways from KEGG and BioCarta. Tools on the site include the GBrowse genome browser, site-wide context dependent search, Connect-the-Dots for connecting gene and other identifiers from multiple data sources, Cytoscape for visualizing and analyzing biological networks, and the GESTALT workbench for genome annotation. All data are open access and all software is open source.