GeneTide--Terra Incognita Discovery Endeavor: a new transcriptome focused member of the GeneCards/GeneNote suite of databases.

GeneCards is an automatically mined database of human genes that strives to create, along with its auxiliary databases--GeneLoc, GeneNote and GeneAnnot--the most inclusive resource of gene-centered information of the human genome. GeneTide, the Gene Terra Incognita Discovery Endeavor (http://genecards.weizmann.

Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification.

Motivation: Genes are often characterized dichotomously as either housekeeping or single-tissue specific. We conjectured that crucial functional information resides in genes with midrange profiles of expression.

Results: To obtain such novel information genome-wide, we have determined the mRNA expression levels for one of the largest hitherto analyzed set of 62 839 probesets in 12 representative normal human tissues.

GeneAnnot: comprehensive two-way linking between oligonucleotide array probesets and GeneCards genes.

Motivation: High density oligonucleotide arrays are usually annotated in a one-to-one fashion, with each probeset assigned to one gene. However, in reality, subsets of oligonucleotides in a probeset may match sequences within more than one gene, potentially leading to misinterpretations. Moreover, a gene is often represented by more than one probeset, and analyzing probe matches at the mRNA level can help one deduce whether these probesets are derived from the same or different splice variants.

GeneNote: whole genome expression profiles in normal human tissues.

A novel data set, GeneNote (Gene Normal Tissue Expression), was produced to portray complete gene expression profiles in healthy human tissues using the Affymetrix GeneChip HG-U95 set, which includes 62 839 probe-sets. The hybridization intensities of two replicates were processed and analyzed to yield the complete transcriptome for twelve human tissues. Abundant novel information on tissue specificity provides a baseline for past and future expression studies related to diseases.

GeneAnnot: interfacing GeneCards with high-throughput gene expression compendia.

The interpretation of microarray expression results often includes extensive efforts to identify and annotate the gene representatives immobilised on the arrays. In this paper we describe the usage of our automatic GeneAnnot system, which links between Affymetrix arrays and the rich human gene annotations available in GeneCards. We explain GeneCards search options and results display; elaborate on the presentation of expression information in GeneCards, including both our whole-genome GeneNote project and external expression resources; describe the various parameters and displays used by GeneAnnot to assess the annotation quality and probeset specificity; and show how to search GeneAnnot and GeneNote websites directly.

GeneLoc: exon-based integration of human genome maps.

Motivation: Despite the numerous available whole-genome mapping resources, no comprehensive, integrated map of the human genome yet exists.

Results: GeneLoc, software adjunct to GeneCards and UDB, integrates gene lists by comparing genomic coordinates at the exon level and assigns unique and meaningful identifiers to each gene.

Human Gene-Centric Databases at the Weizmann Institute of Science: GeneCards, UDB, CroW 21 and HORDE.

Recent enhancements and current research in the GeneCards (GC) (http://bioinfo.weizmann.ac.

GeneCards 2002: towards a complete, object-oriented, human gene compendium.

Motivation: In the post-genomic era, functional analysis of genes requires a sophisticated interdisciplinary arsenal. Comprehensive resources are challenged to provide consistently improving, state-of-the-art tools.

Results: GeneCards (Rebhan et al.