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Vol. 9, Issue 2, 195-209, February 1999

RESOURCE
The Genexpress IMAGE Knowledge Base of the Human Brain Transcriptome: A Prototype Integrated Resource for Functional and Computational Genomics

Geneviève Piétu,1,5 Régine Mariage-Samson,1 Nicole-Adeline Fayein,1 Christiane Matingou,1 Eric Eveno,1 Rémi Houlgatte,1 Charles Decraene,1 Yves Vandenbrouck,1 Fariza Tahi,1 Marie-Dominique Devignes,1 Ute Wirkner,2 Wilhelm Ansorge,2 David Cox,3 Takahiro Nagase,4 Nobuo Nomura,4 and Charles Auffray1

1 Genexpress, Centre National de la Recherche Scientifique (CNRS), 94801 Villejuif, France; 2 European Molecular Biology Laboratory, 6900 Heidelberg, Germany; 3 Stanford Human Genome Center, Stanford University, Stanford, California 94305 USA; 4 Kazusa DNA Research Institute, Kisarazu, Chiba 292 Japan

Expression profiles of 5058 human gene transcripts represented by an array of 7451 clones from the first IMAGE Consortium cDNA library from infant brain have been collected by semiquantitative hybridization of the array with complex probes derived by reverse transcription of mRNA from brain and five other human tissues. Twenty-one percent of the clones corresponded to transcripts that could be classified in general categories of low, moderate, or high abundance. These expression profiles were integrated with cDNA clone and sequence clustering and gene mapping information from an upgraded version of the Genexpress Index. For seven gene transcripts found to be transcribed preferentially or specifically in brain, the expression profiles were confirmed by Northern blot analyses of mRNA from eight adult and four fetal tissues, and 15 distinct regions of brain. In four instances, further documentation of the sites of expression was obtained by in situ hybridization of rat-brain tissue sections. A systematic effort was undertaken to further integrate available cytogenetic, genetic, physical, and genic map informations through radiation-hybrid mapping to provide a unique validated map location for each of these genes in relation to the disease map. The resulting Genexpress IMAGE Knowledge Base is illustrated by five examples presented in the printed article with additional data available on a dedicated Web site at the address http://idefix.upr420.vjf.cnrs.fr/EXPR/welcome.html.

5   Corresponding author.

9:195-209 ©1999 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/99 $5.00
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