title: Computational detection of alternative exon usage.
abstract: BACKGROUND
  With the advent of the GeneChip Exon Arrays, it is now possible to extract "exon-level" expression estimates, allowing for detection of alternative splicing events, one of the primary mechanisms of transcript diversity. In the context of (1) a complex trait use case and (2) a human cerebellum vs. heart comparison on previously validated data, we present a transcript-based statistical model and validation framework to allow detection of alternative exon usage (AEU) between different groups. To illustrate the approach, we detect and confirm differences in exon usage in the two of the most widely studied mouse genetic models (the C57BL/6J and DBA/2J inbred strains) and in a human dataset.
  
  
  RESULTS
  We developed a computational framework that consists of probe level annotation mapping and statistical modeling to detect putative AEU events, as well as visualization and alignment with known splice events. We show a dramatic improvement (∼25 fold) in the ability to detect these events using the appropriate annotation and statistical model which is actually specified at the transcript level, as compared with the transcript cluster/gene-level annotation used on the array. An additional component of this workflow is a probe index that allows ranking AEU candidates for validation and can aid in identification of false positives due to single nucleotide polymorphisms.
  
  
  CONCLUSIONS
  Our work highlights the importance of concordance between the functional unit interrogated (e.g., gene, transcripts) and the entity (e.g., exon, probeset) within the statistical model. The framework we present is broadly applicable to other platforms (including RNAseq).
authors.affiliation: Oregon Clinical Research and Translational Institute, Oregon Health and Science University Portland, OR, USA.
authors.forename: Ted G
authors.initials: TG
authors.lastname: Laderas
authors.forename: Nicole A R
authors.initials: NA
authors.lastname: Walter
authors.forename: Michael
authors.initials: M
authors.lastname: Mooney
authors.forename: Kristina
authors.initials: K
authors.lastname: Vartanian
authors.forename: Priscila
authors.initials: P
authors.lastname: Darakjian
authors.forename: Kari
authors.initials: K
authors.lastname: Buck
authors.forename: Christina A
authors.initials: CA
authors.lastname: Harrington
authors.forename: John
authors.initials: J
authors.lastname: Belknap
authors.forename: Robert
authors.initials: R
authors.lastname: Hitzemann
authors.forename: Shannon K
authors.initials: SK
authors.lastname: McWeeney