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Database Commons - GeneSpeed

GeneSpeed

Citations: 10

z-index 0.00

Short name GeneSpeed
Full name GeneSpeed database
Description GeneSpeed is an online database and resource tool facilitating the detailed study of protein domain homology in the transcriptomes of Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans.
URL http://genespeed.uchsc.edu/
Year founded 2006
Last update & version 2006-11-28    
Availability Not Available
University/Institution hosted University of Colorado at Denver and Health Sciences Center
Address 1775 North Ursula Street, Mail Stop B140, PO Box 6511, Denver, CO, 80045, USA
City Denver
Province/State Colorado
Country/Region United States
Contact name Jan Jensen
Contact email jan.jensen@uchsc.edu
Data type(s)
Major organism(s)
Keyword(s)
  • protein domain homology
  • transcriptome
Publication(s)
  • GeneSpeed: protein domain organization of the transcriptome. [PMID: 17132830]

    Alecksandr Kutchma, Nayeem Quayum, Jan Jensen
    Nucleic acids research 2007:35(Database issue)
    10 Citations (Google Scholar as of 2016-06-09)

    Abstract: The GeneSpeed database (http://genespeed.uchsc.edu/) is an online database and resource tool facilitating the detailed study of protein domain homology in the transcriptomes of Homo sapiens, Mus musculus, Drosophila melanogaster and Caenorhabditis elegans. The population schema for the GeneSpeed database takes advantage of HOWARD parallel cluster technology (http://www.massivelyparallel.com/) and performs exhaustive tBLASTn searches covering all pre-assigned PFAM domain classes in all species (currently 7973 domain families) against the respective Unigene EST databases of the selected four transcriptomes. The resulting database provides a complete annotation of presumed protein domain presence for each Unigene cluster. To complement this domain annotation we have also performed a custom transcription factor-family curation of all Pfam domains, incorporated the Gene Ontology classifications for these domains as well as integrated the Novartis SymAtlas2 dataset for both human and mouse which provides rapid and easy access to tissue-based expression analysis. Consequently, the GeneSpeed database provides the user with the capability to browse or search the database by any of these specialized criteria as well as more traditional means (gene identifier, gene symbol, etc.), thereby enabling a supervised analysis of gene families through a top-down hierarchical basis defined by domain content, all directly linked to an optimized gene expression dataset.

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Tags

Protein RNA
Caenorhabditis elegans Drosophila melanogaster Homo sapiens Mus musculus
protein domain homology transcriptome

Record metadata

  • Created on: 2015-08-10
  • Curated by:
    • Lin Liu [2016-03-26]
    • Jian Sang [2015-12-05]
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