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dc.contributor.authorSood, Sanjanaen_UK
dc.contributor.authorSzkop, Krzysztof Jen_UK
dc.contributor.authorNakhuda, Asifen_UK
dc.contributor.authorGallagher, Iain Jen_UK
dc.contributor.authorMurie, Carlen_UK
dc.contributor.authorBrogan, Robert Jen_UK
dc.contributor.authorKaprio, Jaakkoen_UK
dc.contributor.authorKainulainen, Heikkien_UK
dc.contributor.authorAtherton, Philip Jen_UK
dc.contributor.authorKujala, Urho Men_UK
dc.contributor.authorGustafsson, Thomasen_UK
dc.contributor.authorLarsson, Olaen_UK
dc.contributor.authorTimmons, James Aen_UK
dc.description.abstractDNA microarrays and RNAseq are complementary methods for studying RNA molecules. Current computational methods to determine alternative exon usage (AEU) using such data require impractical visual inspection and still yield high false-positive rates. Integrated Gene and Exon Model of Splicing (iGEMS) adapts a gene-level residuals model with a gene size adjusted false discovery rate and exon-level analysis to circumvent these limitations. iGEMS was applied to two new DNA microarray datasets, including the high coverage Human Transcriptome Arrays 2.0 and performance was validated using RT-qPCR. First, AEU was studied in adipocytes treated with (n = 9) or without (n = 8) the anti-diabetes drug, rosiglitazone. iGEMS identified 555 genes with AEU, and robust verification by RT-qPCR (∼90\%). Second, in a three-way human tissue comparison (muscle, adipose and blood, n = 41) iGEMS identified 4421 genes with at least one AEU event, with excellent RT-qPCR verification (95\%, n = 22). Importantly, iGEMS identified a variety of AEU events, including 3′UTR extension, as well as exon inclusion/exclusion impacting on protein kinase and extracellular matrix domains. In conclusion, iGEMS is a robust method for identification of AEU while the variety of exon usage between human tissues is 5–10 times more prevalent than reported by the Genotype-Tissue Expression consortium using RNA sequencing.en_UK
dc.publisherOxford University Pressen_UK
dc.relationSood S, Szkop KJ, Nakhuda A, Gallagher IJ, Murie C, Brogan RJ, Kaprio J, Kainulainen H, Atherton PJ, Kujala UM, Gustafsson T, Larsson O & Timmons JA (2016) iGEMS: an integrated model for identification of alternative exon usage events. Nucleic Acids Research, 44 (11), Art. No.: e109.
dc.rights© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en_UK
dc.titleiGEMS: an integrated model for identification of alternative exon usage eventsen_UK
dc.typeJournal Articleen_UK
dc.citation.jtitleNucleic Acids Researchen_UK
dc.type.statusVoR - Version of Recorden_UK
dc.contributor.affiliationKing's College Londonen_UK
dc.contributor.affiliationKing's College Londonen_UK
dc.contributor.affiliationKing's College Londonen_UK
dc.contributor.affiliationKarolinska Instituteten_UK
dc.contributor.affiliationXRGenomics Ltden_UK
dc.contributor.affiliationUniversity of Helsinkien_UK
dc.contributor.affiliationUniversity of Jyvaskyla, Finlanden_UK
dc.contributor.affiliationUniversity of Nottinghamen_UK
dc.contributor.affiliationUniversity of Jyvaskyla, Finlanden_UK
dc.contributor.affiliationKarolinska University Hospitalen_UK
dc.contributor.affiliationKarolinska Instituteten_UK
dc.contributor.affiliationKing's College Londonen_UK
rioxxterms.apcnot requireden_UK
rioxxterms.typeJournal Article/Reviewen_UK
local.rioxx.authorSood, Sanjana|en_UK
local.rioxx.authorSzkop, Krzysztof J|en_UK
local.rioxx.authorNakhuda, Asif|en_UK
local.rioxx.authorGallagher, Iain J|0000-0002-8630-7235en_UK
local.rioxx.authorMurie, Carl|en_UK
local.rioxx.authorBrogan, Robert J|en_UK
local.rioxx.authorKaprio, Jaakko|en_UK
local.rioxx.authorKainulainen, Heikki|en_UK
local.rioxx.authorAtherton, Philip J|en_UK
local.rioxx.authorKujala, Urho M|en_UK
local.rioxx.authorGustafsson, Thomas|en_UK
local.rioxx.authorLarsson, Ola|en_UK
local.rioxx.authorTimmons, James A|en_UK
local.rioxx.projectInternal Project|University of Stirling|
local.rioxx.filenameNucl. Acids Res.-2016-Sood-e109.pdfen_UK
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