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 in | Proceedings of the National Academy of Sciences - PNAS Vol. 101; no. 16; pp. 6062 - 6067 |
|---|---|
| Main Authors | , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
National Academy of Sciences
20.04.2004
National Acad Sciences |
| Subjects | |
| Online Access | Get full text |
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| Abstract | 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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| AbstractList | 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. 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. [PUBLICATION ABSTRACT] 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.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. |
| Author | Su, Andrew I. Wiltshire, Tim Hayakawa, Mimi Ching, Keith A. Soden, Richard Cooke, Michael P. Kreiman, Gabriel Vogt, Peter K. Lapp, Hilmar Batalov, Serge Zhang, Jie Walker, John R. Block, David Hogenesch, John B. |
| AuthorAffiliation | The Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Drive, San Diego, CA 92121; and § Department of Neuropharmacology, The Scripps Research Institute, 10550 North Torrey Pines Road, San Diego, CA 92037 |
| AuthorAffiliation_xml | – name: The Genomics Institute of the Novartis Research Foundation, 10675 John J. Hopkins Drive, San Diego, CA 92121; and § Department of Neuropharmacology, The Scripps Research Institute, 10550 North Torrey Pines Road, San Diego, CA 92037 |
| Author_xml | – sequence: 1 givenname: Andrew I. surname: Su fullname: Su, Andrew I. – sequence: 2 givenname: Tim surname: Wiltshire fullname: Wiltshire, Tim – sequence: 3 givenname: Serge surname: Batalov fullname: Batalov, Serge – sequence: 4 givenname: Hilmar surname: Lapp fullname: Lapp, Hilmar – sequence: 5 givenname: Keith A. surname: Ching fullname: Ching, Keith A. – sequence: 6 givenname: David surname: Block fullname: Block, David – sequence: 7 givenname: Jie surname: Zhang fullname: Zhang, Jie – sequence: 8 givenname: Richard surname: Soden fullname: Soden, Richard – sequence: 9 givenname: Mimi surname: Hayakawa fullname: Hayakawa, Mimi – sequence: 10 givenname: Gabriel surname: Kreiman fullname: Kreiman, Gabriel – sequence: 11 givenname: Michael P. surname: Cooke fullname: Cooke, Michael P. – sequence: 12 givenname: John R. surname: Walker fullname: Walker, John R. – sequence: 13 givenname: John B. surname: Hogenesch fullname: Hogenesch, John B. – sequence: 14 givenname: Peter K. surname: Vogt fullname: Vogt, Peter K. |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/15075390$$D View this record in MEDLINE/PubMed |
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| Notes | SourceType-Scholarly Journals-1 ObjectType-Feature-1 content type line 14 ObjectType-Article-2 content type line 23 ObjectType-Article-1 ObjectType-Feature-2 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. |
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| Snippet | The tissue-specific pattern of mRNA expression can indicate important clues about gene function. High-density oligonucleotide arrays offer the opportunity to... |
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| SubjectTerms | 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 |
| Title | A Gene Atlas of the Mouse and Human Protein-Encoding Transcriptomes |
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