The functional landscape of mouse gene expression
<p>Abstract</p> <p>Background</p> <p>Large-scale quantitative analysis of transcriptional co-expression has been used to dissect regulatory networks and to predict the functions of new genes discovered by genome sequencing in model organisms such as yeast. Although the...
| Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2004-12-01
|
| Series: | Journal of Biology |
| Online Access: | http://jbiol.com/content/3/5/21 |
| _version_ | 1828257406883201024 |
|---|---|
| author | Zhang Wen Morris Quaid D Chang Richard Shai Ofer Bakowski Malina A Mitsakakis Nicholas Mohammad Naveed Robinson Mark D Zirngibl Ralph Somogyi Eszter Laurin Nancy Eftekharpour Eftekhar Sat Eric Grigull Jörg Pan Qun Peng Wen-Tao Krogan Nevan Greenblatt Jack Fehlings Michael van der Kooy Derek Aubin Jane Bruneau Benoit G Rossant Janet Blencowe Benjamin J Frey Brendan J Hughes Timothy R |
| author_facet | Zhang Wen Morris Quaid D Chang Richard Shai Ofer Bakowski Malina A Mitsakakis Nicholas Mohammad Naveed Robinson Mark D Zirngibl Ralph Somogyi Eszter Laurin Nancy Eftekharpour Eftekhar Sat Eric Grigull Jörg Pan Qun Peng Wen-Tao Krogan Nevan Greenblatt Jack Fehlings Michael van der Kooy Derek Aubin Jane Bruneau Benoit G Rossant Janet Blencowe Benjamin J Frey Brendan J Hughes Timothy R |
| author_sort | Zhang Wen |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Large-scale quantitative analysis of transcriptional co-expression has been used to dissect regulatory networks and to predict the functions of new genes discovered by genome sequencing in model organisms such as yeast. Although the idea that tissue-specific expression is indicative of gene function in mammals is widely accepted, it has not been objectively tested nor compared with the related but distinct strategy of correlating gene co-expression as a means to predict gene function.</p> <p>Results</p> <p>We generated microarray expression data for nearly 40,000 known and predicted mRNAs in 55 mouse tissues, using custom-built oligonucleotide arrays. We show that quantitative transcriptional co-expression is a powerful predictor of gene function. Hundreds of functional categories, as defined by Gene Ontology 'Biological Processes', are associated with characteristic expression patterns across all tissues, including categories that bear no overt relationship to the tissue of origin. In contrast, simple tissue-specific restriction of expression is a poor predictor of which genes are in which functional categories. As an example, the highly conserved mouse gene <it>PWP1 </it>is widely expressed across different tissues but is co-expressed with many RNA-processing genes; we show that the uncharacterized yeast homolog of <it>PWP1 </it>is required for rRNA biogenesis.</p> <p>Conclusions</p> <p>We conclude that 'functional genomics' strategies based on quantitative transcriptional co-expression will be as fruitful in mammals as they have been in simpler organisms, and that transcriptional control of mammalian physiology is more modular than is generally appreciated. Our data and analyses provide a public resource for mammalian functional genomics.</p> |
| first_indexed | 2024-04-13T02:41:11Z |
| format | Article |
| id | doaj.art-52f28627bc7c4a66bbeebc36ec071bc2 |
| institution | Directory Open Access Journal |
| issn | 1478-5854 1475-4924 |
| language | English |
| last_indexed | 2024-04-13T02:41:11Z |
| publishDate | 2004-12-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Biology |
| spelling | doaj.art-52f28627bc7c4a66bbeebc36ec071bc22022-12-22T03:06:12ZengBMCJournal of Biology1478-58541475-49242004-12-01352110.1186/jbiol16The functional landscape of mouse gene expressionZhang WenMorris Quaid DChang RichardShai OferBakowski Malina AMitsakakis NicholasMohammad NaveedRobinson Mark DZirngibl RalphSomogyi EszterLaurin NancyEftekharpour EftekharSat EricGrigull JörgPan QunPeng Wen-TaoKrogan NevanGreenblatt JackFehlings Michaelvan der Kooy DerekAubin JaneBruneau Benoit GRossant JanetBlencowe Benjamin JFrey Brendan JHughes Timothy R<p>Abstract</p> <p>Background</p> <p>Large-scale quantitative analysis of transcriptional co-expression has been used to dissect regulatory networks and to predict the functions of new genes discovered by genome sequencing in model organisms such as yeast. Although the idea that tissue-specific expression is indicative of gene function in mammals is widely accepted, it has not been objectively tested nor compared with the related but distinct strategy of correlating gene co-expression as a means to predict gene function.</p> <p>Results</p> <p>We generated microarray expression data for nearly 40,000 known and predicted mRNAs in 55 mouse tissues, using custom-built oligonucleotide arrays. We show that quantitative transcriptional co-expression is a powerful predictor of gene function. Hundreds of functional categories, as defined by Gene Ontology 'Biological Processes', are associated with characteristic expression patterns across all tissues, including categories that bear no overt relationship to the tissue of origin. In contrast, simple tissue-specific restriction of expression is a poor predictor of which genes are in which functional categories. As an example, the highly conserved mouse gene <it>PWP1 </it>is widely expressed across different tissues but is co-expressed with many RNA-processing genes; we show that the uncharacterized yeast homolog of <it>PWP1 </it>is required for rRNA biogenesis.</p> <p>Conclusions</p> <p>We conclude that 'functional genomics' strategies based on quantitative transcriptional co-expression will be as fruitful in mammals as they have been in simpler organisms, and that transcriptional control of mammalian physiology is more modular than is generally appreciated. Our data and analyses provide a public resource for mammalian functional genomics.</p>http://jbiol.com/content/3/5/21 |
| spellingShingle | Zhang Wen Morris Quaid D Chang Richard Shai Ofer Bakowski Malina A Mitsakakis Nicholas Mohammad Naveed Robinson Mark D Zirngibl Ralph Somogyi Eszter Laurin Nancy Eftekharpour Eftekhar Sat Eric Grigull Jörg Pan Qun Peng Wen-Tao Krogan Nevan Greenblatt Jack Fehlings Michael van der Kooy Derek Aubin Jane Bruneau Benoit G Rossant Janet Blencowe Benjamin J Frey Brendan J Hughes Timothy R The functional landscape of mouse gene expression Journal of Biology |
| title | The functional landscape of mouse gene expression |
| title_full | The functional landscape of mouse gene expression |
| title_fullStr | The functional landscape of mouse gene expression |
| title_full_unstemmed | The functional landscape of mouse gene expression |
| title_short | The functional landscape of mouse gene expression |
| title_sort | functional landscape of mouse gene expression |
| url | http://jbiol.com/content/3/5/21 |
| work_keys_str_mv | AT zhangwen thefunctionallandscapeofmousegeneexpression AT morrisquaidd thefunctionallandscapeofmousegeneexpression AT changrichard thefunctionallandscapeofmousegeneexpression AT shaiofer thefunctionallandscapeofmousegeneexpression AT bakowskimalinaa thefunctionallandscapeofmousegeneexpression AT mitsakakisnicholas thefunctionallandscapeofmousegeneexpression AT mohammadnaveed thefunctionallandscapeofmousegeneexpression AT robinsonmarkd thefunctionallandscapeofmousegeneexpression AT zirngiblralph thefunctionallandscapeofmousegeneexpression AT somogyieszter thefunctionallandscapeofmousegeneexpression AT laurinnancy thefunctionallandscapeofmousegeneexpression AT eftekharpoureftekhar thefunctionallandscapeofmousegeneexpression AT sateric thefunctionallandscapeofmousegeneexpression AT grigulljorg thefunctionallandscapeofmousegeneexpression AT panqun thefunctionallandscapeofmousegeneexpression AT pengwentao thefunctionallandscapeofmousegeneexpression AT krogannevan thefunctionallandscapeofmousegeneexpression AT greenblattjack thefunctionallandscapeofmousegeneexpression AT fehlingsmichael thefunctionallandscapeofmousegeneexpression AT vanderkooyderek thefunctionallandscapeofmousegeneexpression AT aubinjane thefunctionallandscapeofmousegeneexpression AT bruneaubenoitg thefunctionallandscapeofmousegeneexpression AT rossantjanet thefunctionallandscapeofmousegeneexpression AT blencowebenjaminj thefunctionallandscapeofmousegeneexpression AT freybrendanj thefunctionallandscapeofmousegeneexpression AT hughestimothyr thefunctionallandscapeofmousegeneexpression AT zhangwen functionallandscapeofmousegeneexpression AT morrisquaidd functionallandscapeofmousegeneexpression AT changrichard functionallandscapeofmousegeneexpression AT shaiofer functionallandscapeofmousegeneexpression AT bakowskimalinaa functionallandscapeofmousegeneexpression AT mitsakakisnicholas functionallandscapeofmousegeneexpression AT mohammadnaveed functionallandscapeofmousegeneexpression AT robinsonmarkd functionallandscapeofmousegeneexpression AT zirngiblralph functionallandscapeofmousegeneexpression AT somogyieszter functionallandscapeofmousegeneexpression AT laurinnancy functionallandscapeofmousegeneexpression AT eftekharpoureftekhar functionallandscapeofmousegeneexpression AT sateric functionallandscapeofmousegeneexpression AT grigulljorg functionallandscapeofmousegeneexpression AT panqun functionallandscapeofmousegeneexpression AT pengwentao functionallandscapeofmousegeneexpression AT krogannevan functionallandscapeofmousegeneexpression AT greenblattjack functionallandscapeofmousegeneexpression AT fehlingsmichael functionallandscapeofmousegeneexpression AT vanderkooyderek functionallandscapeofmousegeneexpression AT aubinjane functionallandscapeofmousegeneexpression AT bruneaubenoitg functionallandscapeofmousegeneexpression AT rossantjanet functionallandscapeofmousegeneexpression AT blencowebenjaminj functionallandscapeofmousegeneexpression AT freybrendanj functionallandscapeofmousegeneexpression AT hughestimothyr functionallandscapeofmousegeneexpression |