T1DBase: integration and presentation of complex data for type 1 diabetes research - PubMed (original) (raw)
. 2007 Jan;35(Database issue):D742-6.
doi: 10.1093/nar/gkl933. Epub 2006 Dec 14.
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
Affiliations
- PMID: 17169983
- PMCID: PMC1781218
- DOI: 10.1093/nar/gkl933
T1DBase: integration and presentation of complex data for type 1 diabetes research
Erin M Hulbert et al. Nucleic Acids Res. 2007 Jan.
Erratum in
- Nucleic Acids Res. 2007;35(18):6338. Cassen, Victor M [added]
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.
Figures
Figure 1
Microarray Viewer showing differential expression of a list of genes across several experiments. The figure shows the default heatmap and profile chart displays of the data. Actual data values can be seen by clicking on the Data view tab. The data can be filtered, clustered, or downloaded by clicking on tabs near the bottom of the figure.
References
- Burren O.S., Healy B.C., Lam A.C., Schuilenburg H., Dolman G.E., Everett V.H., Laneri D., Nutland S., Rance H.E., Payne F., et al. Development of an integrated genome informatics, data management and workflow infrastructure: A toolbox for the study of complex disease. Hum. Genomics. 2004;1:98–109. - PMC - PubMed
- Kaestner K.H., Lee C.S., Scearce L.M., Brestelli J.E., Arsenlis A., Le P.P., Lantz K.A., Crabtree J., Pizarro A., Mazzarelli J., et al. Transcriptional program of the endocrine pancreas in mice and humans. Diabetes. 2003;52:1604–1610. - PubMed
- Goodman N., McCormick K., Goldowitz D., Hockly E., Johnson C., Kristal B., MacDonald M., Truant R., Beuzekom M.V. Plans for HDBase—a research community website for Huntington's disease. Clin. Neurosci. Res. 2003;3:197–217.
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