A Gene Atlas of the Mouse and Human Protein-Encoding Transcriptomes

The tissue-specific pattern of mRNA expression can indicate important clues about gene function. High-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale. Toward this end, we have designed custom arrays that interrogate the expression of the...

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Published inProceedings of the National Academy of Sciences - PNAS Vol. 101; no. 16; pp. 6062 - 6067
Main Authors Su, Andrew I., Wiltshire, Tim, Batalov, Serge, Lapp, Hilmar, Ching, Keith A., Block, David, Zhang, Jie, Soden, Richard, Hayakawa, Mimi, Kreiman, Gabriel, Cooke, Michael P., Walker, John R., Hogenesch, John B., Vogt, Peter K.
Format Journal Article
LanguageEnglish
Published United States National Academy of Sciences 20.04.2004
National Acad Sciences
Subjects
Animals
Biological Sciences
Chromosomes
Datasets
Female
Gene expression
Genes
Genetic loci
Genetic research
Genetics
Genomes
Genomic Imprinting
Genomics
Humans
Male
Mice
Proteins
RNA
RNA, Messenger - genetics
Transcription, Genetic
Transcriptomes
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Summary:The tissue-specific pattern of mRNA expression can indicate important clues about gene function. High-density oligonucleotide arrays offer the opportunity to examine patterns of gene expression on a genome scale. Toward this end, we have designed custom arrays that interrogate the expression of the vast majority of protein-encoding human and mouse genes and have used them to profile a panel of 79 human and 61 mouse tissues. The resulting data set provides the expression patterns for thousands of predicted genes, as well as known and poorly characterized genes, from mice and humans. We have explored this data set for global trends in gene expression, evaluated commonly used lines of evidence in gene prediction methodologies, and investigated patterns indicative of chromosomal organization of transcription. We describe hundreds of regions of correlated transcription and show that some are subject to both tissue and parental allele-specific expression, suggesting a link between spatial expression and imprinting.
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A.I.S., T.W., and S.B. contributed equally to this work.
Present address: Center for Biological and Computational Learning, Massachusetts Institute of Technology, MIT E25-201, Cambridge, MA 02142.
Edited by Peter K. Vogt, The Scripps Research Institute, La Jolla, CA
This paper was submitted directly (Track II) to the PNAS office.
To whom correspondence should be addressed. E-mail: hogenesch@gnf.org.
Abbreviations: RCT, regions of correlated transcription; AUC, area under the curve; LCR, locus control regions.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.0400782101