Extent and diversity of human alternative splicing established by complementary database annotation and microarray analysis

Jonathan L. Bingham, Patricia E. Carrigan, Laurence J Miller, Subha Srinivasan

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

Alternative splicing generates functional diversity in higher organisms through alternative first and last exons, skipped and included exons, intron retentions and alternative donor, and acceptor sites. In large-scale microarray studies in humans and the mouse, emphasis so far has been placed on exon-skip events, leaving the prevalence and importance of other splice types largely unexplored. Using a new human splice variant database and a genome-wide microarray to probes thousands of splice events of each type, we measured differential expression of splice types across six pair of diverse cell lines and validated the database annotation process. Results suggest that splicing in humans is more complex than simple exon-skip events, which account for a minority of splicing differences. The relative frequency of differential expression of the splice types correlates with what is found by our annotation efforts. In conclusion, alternative splicing in human cells is considerably more complex than the canonical example of the exon skip. The complementary approaches of genome-wide annotation of alternative splicing in human and design of genome-wide splicing microarrays to measure differential splicing in biological samples provide a powerful high-throughput tool to study the role of alternative splicing in human biology.

Original languageEnglish (US)
Pages (from-to)83-92
Number of pages10
JournalOMICS A Journal of Integrative Biology
Volume12
Issue number1
DOIs
StatePublished - Mar 1 2008

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Alternative Splicing
Microarray Analysis
Microarrays
Exons
Databases
Genes
Cells
Genome
Human Genome
Introns
Throughput
Cell Line

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Extent and diversity of human alternative splicing established by complementary database annotation and microarray analysis. / Bingham, Jonathan L.; Carrigan, Patricia E.; Miller, Laurence J; Srinivasan, Subha.

In: OMICS A Journal of Integrative Biology, Vol. 12, No. 1, 01.03.2008, p. 83-92.

Research output: Contribution to journalArticle

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