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Exon Array Analysis Changing the Landscape of Gene Expresson Profiling. Tzu L. Phang Ph. D. Department of Medicine Division of Pulmonary Sciences and Critical Care Medicine. Alternative Splicing (AS). important regulatory mechanism in gene expression Estimated 70% of all genes undergo AS

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exon array analysis changing the landscape of gene expresson profiling

Exon Array AnalysisChanging the Landscape of Gene Expresson Profiling

Tzu L. Phang Ph. D.

Department of Medicine

Division of Pulmonary Sciences and Critical Care Medicine

alternative splicing as
Alternative Splicing (AS)
  • important regulatory mechanism in gene expression
  • Estimated 70% of all genes undergo AS
  • About 15% of AS known to cause some form of genetic disease.
slide3
Exon 1.0 ST

5.4 millions, 5 m features

1.4 millions probesets (exon)

3 gene level annotations:

Core: 17 K genes

RefSeq and full length mRNA

Extended: 129 K genes

Core + cDNA-based annotation

Full: 262 K genes

Extended + ab-initio gene predictions

HG_U133plus2

1.3 millions, 11 m features

54,000 probeset (gene)

exon array analysis work flow
Exon Array Analysis Work Flow

A positive SI unit indicate higher inclusion rate for the exon in

sample 1, or low-expression for the exon in sample 2

slide5

Results

http://xmap.picr.man.ac.uk/

wide opened areas
Wide opened areas:
  • Compare different detection methods
    • ANOSVA, ASAP, GenASAP, SPLICE, etc
  • Develop algorithm to mine the noisy data
  • Cluster genes into similar alternative splice forms
    • Splicing graphs, modeling approaches, etc
  • Functional impact analysis of alternative splicing
  • Discovery of miRNA (intergenic regions)
  • Impact of SNiP on alternative splicing detection