HCNetDat is a DNA microarray gene annotation database. The Hartwell Center for Bioinformatics and Biotechnology developed HCNetDat to provide St. Jude investigators with the most current gene annotation possible for genes present on commonly used Affymetrix GeneChips ™ and spotted cDNA arrays designed and produced in the Hartwell Center. Thousands of database searches against NCBIís RefSeq and Genbank were conducted to obtain the most current annotation information. The database contains annotations for genes represented in Incyte's Mouse release 1.0 and UniGene 1.0 cDNA libraries, Incyte's UniGene1.0 human cDNA library, the BMAP Retinal mouse cDNA library and the Affymetrix ™ mouse U74Av2, mouse Moe430, human U95Av2, human U133A/B and Plus 2.0 sets, and yeast YG-S98 GeneChips. One can query by keywords, accession numbers, probe-set IDs, and search by physical or chromosome location. One can compare arrays and download lists of genes common or unique between any two selected microarrays. One can submit lists of probe-set IDs to identify the chip(s) on which they are located. Human-Mouse orthologs, along with their pair-wise sequence alignment, are provided for most of the annotated genes in the database. It is our intention to update the database regularly so that you have the most accurate and current data possible.
New features in HCNetDat version 2.2 (May 15, 2004):
A MapViewer added for visual display of genes on chromosomes (currently for Human genes only).
Complete coverage of the Human Genome U133 Set plus 6,500 additional genes for analysis of over 47,000 transcripts.
The Human Genome U133 Set represents more than 39,000 transcripts derived from approximately 33,000 well-substantiated human genes. The clusters were created from the UniGene database (Build 133, April 2001).
The Human Genome U95 Set represents approximately 54,000 clusters derived from the UniGene database (Build 95).
Complete coverage of the GeneChip(r) Mouse Expression Set 430 for analysis of over 39,000 transcripts on a single array.
The Murine Genome Moe430 Set represents approximately 34,000 full-length mouse genes and EST clusters. The sequence clusters were created from the UniGene database (Build 107, June 2002).
The Murine Genome U74v2 Set represents approximately 36,000 full-length mouse genes and EST clusters from the UniGene database (Build 74).
The Yeast Genome S98 Array contains probe sets for approximately 6,400 S. cerevisiae (S288C strain) genes identified in the Saccharomyces Genome Database (December 1998). This array also contains approximately 600 additional probe sets representing putative open reading frames (ORFs) identified by SAGE analysis, mitochondrial proteins, TY proteins, plasmids, and a small number of ORFs for strains other than S288C.