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. DISCUSSION: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).
journal_name
Front Neuroscijournal_title
Frontiers in neuroscienceauthors
Laderas TG,Walter NA,Mooney M,Vartanian K,Darakjian P,Buck K,Harrington CA,Belknap J,Hitzemann R,McWeeney SKdoi
10.3389/fnins.2011.00069subject
Has Abstractpub_date
2011-05-13 00:00:00pages
69eissn
1662-4548issn
1662-453Xjournal_volume
5pub_type
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journal_title:Frontiers in neuroscience
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journal_title:Frontiers in neuroscience
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journal_title:Frontiers in neuroscience
pub_type: 杂志文章
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更新日期:2010-05-15 00:00:00
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pub_type: 杂志文章
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journal_title:Frontiers in neuroscience
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doi:10.3389/fnins.2017.00262
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journal_title:Frontiers in neuroscience
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pub_type: 杂志文章
doi:10.3389/fnins.2018.00550
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pub_type: 杂志文章,评审
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更新日期:2013-12-18 00:00:00
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journal_title:Frontiers in neuroscience
pub_type: 杂志文章
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abstract::[This corrects the article DOI: 10.3389/fnins.2019.00413.]. ...
journal_title:Frontiers in neuroscience
pub_type: 已发布勘误
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更新日期:2019-08-28 00:00:00
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