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. 2005 Jan 1;33(Database issue):D544-9.
doi: 10.1093/nar/gki095.

T1DBase, a community web-based resource for type 1 diabetes research

Luc J Smink  1 , 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
Affiliations

T1DBase, a community web-based resource for type 1 diabetes research

Luc J Smink et al. Nucleic Acids Res. .

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.

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Figures

Figure 1
Figure 1
T1DBase homepage. Most pages have a similar format. The T1DBase icon in the top banner returns the user to the homepage. The search box in the upper right corner lets the user search the entire site. Tabs below the search box provide access to related pages. The history links directly below the T1DBase icon allow return to past pages. The navigation bar on the left provides links to the different areas of the site. On the homepage, users can navigate to specific chromosomes or T1D susceptibility regions by clicking on the ideogram. Each page has a footer with links to our privacy policy and other legal fine print.
Figure 2
Figure 2
Display of NOD congenic strain A graphical representation of strain c3c4, Taconic line 1112, showing B6 and B10 DNA introgressed into an NOD background as a blue bar. The B6/B10 haplotype boundary markers for the introgressed DNA are shown in green and the NOD boundary markers in red. The regions between known B6 or B10 and known NOD DNA are shaded gray. The Idd designations for the chromosomes shown are displayed in their relative positions. A scale is provided for each chromosome to show genomic location of markers and Idd regions.
Figure 3
Figure 3
GBrowse display of CBLB gene showing several tracks: the genome tile path, mouse and rat highly conserved regions, Ensembl and DIL transcript annotations, DIL SNP typology, mRNA homology and regulatory potential. Other data track can be switched on using controls on the web page (data not shown).
See this image and copyright information in PMC

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