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Exp Diabetes Res. 2008;2008:312060. doi: 10.1155/2008/312060.

GeneSpeed Beta Cell: an online genomics data repository and analysis resource tailored for the islet cell biologist.

Author information

  • 1Barbara Davis Center for Childhood Diabetes, University of Colorado, HSC., 1775 Ursula Street, B140, Aurora, CO 80045, USA.

Abstract

OBJECTIVE:

We here describe the development of a freely available online database resource, GeneSpeed Beta Cell, which has been created for the pancreatic islet and pancreatic developmental biology investigator community.

RESEARCH DESIGN AND METHODS:

We have developed GeneSpeed Beta Cell as a separate component of the GeneSpeed database, providing a genomics-type data repository of pancreas and islet-relevant datasets interlinked with the domain-oriented GeneSpeed database.

RESULTS:

GeneSpeed Beta Cell allows the query of multiple published and unpublished select genomics datasets in a simultaneous fashion (multiexperiment viewing) and is capable of defining intersection results from precomputed analysis of such datasets (multidimensional querying). Combined with the protein-domain categorization/assembly toolbox provided by the GeneSpeed database, the user is able to define spatial expression constraints of select gene lists in a relatively rigid fashion within the pancreatic expression space. We provide several demonstration case studies of relevance to islet cell biology and development of the pancreas that provide novel insight into islet biology.

CONCLUSIONS:

The combination of an exhaustive domain-based compilation of the transcriptome with gene array data of interest to the islet biologist affords novel methods for multidimensional querying between individual datasets in a rapid fashion, presently not available elsewhere.

PMID:
18795106
[PubMed - indexed for MEDLINE]
PMCID:
PMC2532782
Free PMC Article
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