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.

Network analysis of protein structures identifies functional residues.

Identifying active site residues strictly from protein three-dimensional structure is a difficult task, especially for proteins that have few or no homologues. We transformed protein structures into residue interaction graphs (RIGs), where amino acid residues are graph nodes and their interactions with each other are the graph edges. We found that active site, ligand-binding and evolutionary conserved residues, typically have high closeness values.

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.