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. Indeed, when using a newly defined graded tissue specificity index tau, valued between 0 for housekeeping genes and 1 for tissue-specific genes, genes with midrange profiles having 0.15< tau<0.85 were found to constitute >50% of all expression patterns. We developed a binary classification, indicating for every gene the I(B) tissues in which it is overly expressed, and the 12-I(B) tissues in which it shows low expression. The 85 dominant midrange patterns with I(B)=2-11 were found to be bimodally distributed, and to contribute most significantly to the definition of tissue specification dendrograms. Our analyses provide a novel route to infer expression profiles for presumed ancestral nodes in the tissue dendrogram. Such definition has uncovered an unsuspected correlation, whereby de novo enhancement and diminution of gene expression go hand in hand. These findings highlight the importance of gene suppression events, with implications to the course of tissue specification in ontogeny and phylogeny. AVAILABILITY: All data and analyses are publically available at the GeneNote website, http://genecards.weizmann.ac.il/genenote/ and, GEO accession GSE803. CONTACT: doron.lancet@weizmann.ac.il SUPPLEMENTARY INFORMATION: Four tables available at the above site.

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.ac.il/genetide/), the newest addition to this family, is a transcriptome-focused database which aims to enhance GeneCards with additional expressed sequence tag (EST)-based genes. This is achieved by comprehensively mapping >85% of the approximately 5.6 million human ESTs currently available at dbEST to known genes by means of data mining and integration of genomic resources including UniGene, DoTS, AceView and in-house resources. GeneTide thus creates comprehensive links between ESTs and GeneCards genes. Furthermore, groups of unassociated transcripts serve as a basis for defining novel EST-based GeneCards Candidates (EGCs). These EGCs, nearly 25,000 of which were defined in version 0.3 of GeneTide, are further annotated with various parameters, including splicing evidence and expression data extracted from the GeneNote database, to determine their validity as possible de novo genes.

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. Residues with high closeness values interact directly or by a few intermediates with all other residues of the protein. Combining closeness and surface accessibility identified active site residues in 70% of 178 representative structures. Detailed structural analysis of specific enzymes also located other types of functional residues. These include the substrate binding sites of acetylcholinesterases and subtilisin, and the regions whose structural changes activate MAP kinase and glycogen phosphorylase. Our approach uses single protein structures, and does not rely on sequence conservation, comparison to other similar structures or any prior knowledge. Residue closeness is distinct from various sequence and structure measures and can thus complement them in identifying key protein residues. Closeness integrates the effect of the entire protein on single residues. Such natural structural design may be evolutionary maintained to preserve interaction redundancy and contribute to optimal setting of functional sites.

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. RESULTS: The GeneAnnot system comprehensively documents the many-to-many relationship between oligonucleotide array probesets and annotated genes in GeneCards. It performs pairwise alignments between the probe sequences and gene transcripts, and assigns sensitivity and specificity scores to each probeset/gene pair. AVAILABILITY: http://genecards.weizmann.ac.il/geneannot/ SUPPLEMENTARY INFORMATION: Program description and statistics http://genecards.weizmann.ac.il/geneannot/DOC/index.html