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Exon Array Analysis Changing the Landscape of Gene Expresson Profiling

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

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  1. 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

  2. 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.

  3. 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)

  4. 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

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

  6. 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

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