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GeneNote


NAR Molecular Biology Database Collection entry number 325
Shmueli, O., Shmoish, M., Rosen, N., Benjamin-Rodrig, H., Yanai, I., Ophir, R., Shklar, M., Almashanu, L., Madi, A., Sirota, A., Kats, P., Chalifa-Caspi, V., Safran, M., Lancet, D.
Departments of Molecular Genetics and Biological Services (Bioinformatics Unit), The Weizmann Institute of Science, 76100, Rehovot, Israel

Database Description

GeneNote is a database of gene expression in normal adult human tissues, based on in-house DNA array experiments using Affymetrix GeneChip HG-U95A-E (http://www.affymetrix.com/analysis/index.affx).

The goals of the project are as follows:
  • to create a tissue expression profile for each human gene
  • to learn about the function of unknown genes from the similarities in their expression profiles to those of known genes
  • to create tissue specificity scores for each gene.
GeneNote currently provides expression tissue vectors for each GeneCards (http://www.genecards.org) gene for the following tissues: bone marrow, brain, heart, kidney, liver, lung, pancreas, prostate, skeletal muscle, spinal cord, spleen, and thymus, all color-coded into the immune, nervous, muscle and secretory system groups. Two replicates are provided for each tissue.

To reflect a quality measure, variation plots are also presented, which visualize Pearson's correlations between individual probe-set tissue vectors and the average tissue vector for each gene, as well as relative scalar lengths of individual vectors. In addition to experimental results, in silico gene expression was calculated for GeneCards by mining the Unigene database for information about the number of unique clones per gene per tissue, and the data presented on a root scale designed to be visually parallel with the experimental tissue vectors.

Expanding beyond the GeneCards gene-centric view, the GeneNote web site provides additional detailed information on a probe-set basis including links to GeneAnnot (http://genecards.weizmann.ac.il/geneannot), and will offer a variety of specialized searching and clustering options. For the list of GeneNote?GeneCards publications, see http://www.genecards.org/publications.html.


Go to the abstract in the NAR 2003 Database Issue.
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