GeneSpeed: protein domain organization of the transcriptome.
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.
Kutchma
Alecksandr
A
Barbara Davis Center for Childhood Diabetes, University of Colorado at Denver and Health Sciences Center, 1775 North Ursula Street, Mail Stop B140, PO Box 6511, Denver, CO, 80045, USA.
Quayum
Nayeem
N
Jensen
Jan
J
D000818:Animals; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry; D030562:Databases, Protein; D029721:Drosophila Proteins / Q000737:chemistry; D020869:Gene Expression Profiling; D006801:Humans; D020407:Internet; D051379:Mice; D017434:Protein Structure, Tertiary / Q000235:genetics; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000737:chemistry; D014158:Transcription, Genetic; D014584:User-Computer Interface
D029742:Caenorhabditis elegans Proteins; D029721:Drosophila Proteins; D014157:Transcription Factors