title: Genome-wide analysis of mouse transcripts using exon microarrays and factor graphs.
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.
authors.affiliation: Electrical and Computer Engineering, University of Toronto, 10 King's College Rd., Toronto, Ontario M5S 3G4, Canada. frey@psi.toronto.edu
authors.forename: Brendan J
authors.initials: BJ
authors.lastname: Frey
authors.forename: Naveed
authors.initials: N
authors.lastname: Mohammad
authors.forename: Quaid D
authors.initials: QD
authors.lastname: Morris
authors.forename: Wen
authors.initials: W
authors.lastname: Zhang
authors.forename: Mark D
authors.initials: MD
authors.lastname: Robinson
authors.forename: Sanie
authors.initials: S
authors.lastname: Mnaimneh
authors.forename: Richard
authors.initials: R
authors.lastname: Chang
authors.forename: Qun
authors.initials: Q
authors.lastname: Pan
authors.forename: Eric
authors.initials: E
authors.lastname: Sat
authors.forename: Janet
authors.initials: J
authors.lastname: Rossant
authors.forename: Benoit G
authors.initials: BG
authors.lastname: Bruneau
authors.forename: Jane E
authors.initials: JE
authors.lastname: Aubin
authors.forename: Benjamin J
authors.initials: BJ
authors.lastname: Blencowe
authors.forename: Timothy R
authors.initials: TR
authors.lastname: Hughes
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D018076:DNA, Complementary / Q000737:chemistry*; D019992:Databases as Topic; D005091:Exons / Q000235:genetics*; D020869:Gene Expression Profiling; D016678:Genome; D006801:Humans; D051379:Mice; D046228:Microarray Analysis; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D018076:DNA, Complementary; D012333:RNA, Messenger