Computational genome-wide discovery of aberrant splice variations with exon expression profiles

Ryo Yoshida, Kazuyuki Numata, Seiya Imoto, Masao Nagasaki, Atsushi Doi, Kazuko Ueno, Satoru Miyano

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

Alternative splicing plays a prominent role in eukaryotic gene regulations that allow a single gene to generate the multiple mRNA products. The recent advent of GeneChip® Human Exon 1.0 ST Array enables us to measure the exon expression profiles of human cells on a genome-wide scale. With this advent, analysis of functional gene regulation could be extended to detect not only differentially expressed genes, but also specific splicing events that occur in target cells, but not in normal controls. We address some statistical issues for the identification of biomarker splice variations with exon expression data. The proposed method involves the following steps: (1) Whole transcript analysis with the nonparametric analysis of variance (ANOVA) to identify potential biomarkers that present specific splice variations. (2) Meta-analysis for discriminating non-specific splice variations that are caused by clinical heterogeneity in the collected samples. In the analysis of human cells, controlling non-specific splicing factors is essential for success in the detection of biomarker splice variations because splice patterns are possibly affected by inter-individual differences in the collected samples. We demonstrate its utility and perform a whole transcript analysis of exon expression profiles of colorectal carcinoma.

Original languageEnglish
Title of host publicationProceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
Pages715-722
Number of pages8
DOIs
Publication statusPublished - 2007 Dec 1
Event7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE - Boston, MA, United States
Duration: 2007 Jan 142007 Jan 17

Publication series

NameProceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

Other

Other7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE
CountryUnited States
CityBoston, MA
Period07/1/1407/1/17

ASJC Scopus subject areas

  • Biotechnology
  • Genetics
  • Bioengineering

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