Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs (original) (raw)

• Letter
• Published: 28 August 2005
• Naveed Mohammad2 na1,
• Quaid D Morris1,2 na1,
• Wen Zhang2,3 na1,
• Mark D Robinson1,2,
• Sanie Mnaimneh2,
• Richard Chang2,
• Qun Pan2,
• Eric Sat4,
• Janet Rossant3,4,
• Benoit G Bruneau3,5,
• Jane E Aubin3,
• Benjamin J Blencowe2,3 &
• …
• Timothy R Hughes2,3

Nature Genetics volume 37, pages 991–996 (2005)Cite this article

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Abstract

Recent mammalian microarray experiments detected widespread transcription and indicated that there may be many undiscovered multiple-exon protein-coding genes. To explore this possibility, we labeled cDNA from unamplified, polyadenylation-selected RNA samples from 37 mouse tissues to microarrays encompassing 1.14 million exon probes. We analyzed these data using GenRate, a Bayesian algorithm that uses a genome-wide scoring function in a factor graph to infer genes. At a stringent exon false detection rate of 2.7%, GenRate detected 12,145 gene-length transcripts and confirmed 81% of the 10,000 most highly expressed known genes. Notably, our analysis showed that most of the 155,839 exons detected by GenRate were associated with known genes, providing microarray-based evidence that most multiple-exon genes have already been identified. GenRate also detected tens of thousands of potential new exons and reconciled discrepancies in current cDNA databases by 'stitching' new transcribed regions into previously annotated genes.

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Acknowledgements

We thank G.E. Hinton for conversations and C. Boone and B. Andrews for their support. This work was supported by grants from the Canadian Institutes of Health Research, the Natural Sciences and Engineering Research Council of Canada and the Canadian Foundation for Innovation (to T.R.H., B.J.F. and B.J.B.), by a PREA award (to B.J.F.) and by a Natural Sciences and Engineering Research Council of Canada postdoctoral fellowship (to Q.D.M.).

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Author notes

1. Brendan J Frey, Naveed Mohammad, Quaid D Morris and Wen Zhang: These authors contributed equally to this work.

Authors and Affiliations

1. Electrical and Computer Engineering, University of Toronto, 10 King's College Rd., Toronto, M5S 3G4, Ontario, Canada
   Brendan J Frey, Quaid D Morris & Mark D Robinson
2. Banting and Best Department of Medical Research, University of Toronto, 112 College St., Toronto, M5G 1L6, Ontario, Canada
   Brendan J Frey, Naveed Mohammad, Quaid D Morris, Wen Zhang, Mark D Robinson, Sanie Mnaimneh, Richard Chang, Qun Pan, Benjamin J Blencowe & Timothy R Hughes
3. Medical Genetics and Microbiology, University of Toronto, 1 King's College Ct., Toronto, M5S 3G4, Ontario, Canada
   Wen Zhang, Janet Rossant, Benoit G Bruneau, Jane E Aubin, Benjamin J Blencowe & Timothy R Hughes
4. Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, M5G 1X5, Ontario, Canada
   Eric Sat & Janet Rossant
5. The Hospital for Sick Children, 555 University Ave., Toronto, M5G 1X8, Ontario, Canada
   Benoit G Bruneau

Authors

1. Brendan J Frey
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2. Naveed Mohammad
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3. Quaid D Morris
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4. Wen Zhang
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5. Mark D Robinson
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6. Sanie Mnaimneh
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7. Richard Chang
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8. Qun Pan
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9. Eric Sat
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10. Janet Rossant
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11. Benoit G Bruneau
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12. Jane E Aubin
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13. Benjamin J Blencowe
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14. Timothy R Hughes
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Corresponding authors

Correspondence toBenjamin J Blencowe or Timothy R Hughes.

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Frey, B., Mohammad, N., Morris, Q. et al. Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs.Nat Genet 37, 991–996 (2005). https://doi.org/10.1038/ng1630

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• Received: 17 June 2005
• Accepted: 28 July 2005
• Published: 28 August 2005
• Issue Date: 01 September 2005
• DOI: https://doi.org/10.1038/ng1630

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