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Expression Analysis Platforms

Expression Analysis Platforms. Outline . What is expression Platforms ChIP on Chip Gene expression Exon arrays Tiling arrays SNP chips Applied S/W for Expression "Library" -- OTDB Alternative Splicing Association Study Example -- AMD How to analyze Applied S/W -- UIMaDS

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Expression Analysis Platforms

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  1. Expression Analysis Platforms

  2. Outline • What is expression • Platforms • ChIP on Chip • Gene expression • Exon arrays • Tiling arrays • SNP chips • Applied S/W for Expression "Library" -- OTDB • Alternative Splicing • Association Study Example -- AMD • How to analyze • Applied S/W -- UIMaDS • Genotype - Phenotype Correlations

  3. Ocular Tissue Expression Database Survey of 10 ocular tissues GOAL: catalog which genes are expressed across tissues of specific interest in ocular In collaboration with Abe Clark at Alcon

  4. Ocular Tissue Expression Database

  5. Ocular Tissue Expression Database

  6. Alternative Splicing in the Eye GOAL: To identify the splicing variants expressed in retina, retinal pigment epithelia, and optic nerve head. (3x biological replicates) Motivation: To guide/focus screening efforts to those exons that are expressed. In collaboration with Rob Mullins

  7. Show Probes

  8. AMD Association Study GOAL: Identify the major susceptibility regions for age-related macular degeneration. Several regions have been reported • How may susceptibility regions are there? Genotyping 400 AMD patients and controls with high-density SNP chips 400,000,000 genotypes

  9. Association populations Unaffected Affected allele frequencies A1 A2 A1 A2 SNP 1 0.74 0.26 0.75 0.25 SNP 2 0.70 0.30 0.10 0.90 Power increases with more samples, and more SNPs

  10. How to analyze the data? First step is acquiring the data! Normalization Analysis

  11. Analysis Differential Expression t-test ANOVA Fold-change Time series (all of the above) Correlation of expression Early response vs. late response

  12. Analysis DAVID Database for Annotation, Visualization and Integrated Discovery http://david.abcc.ncifcrf.gov/ • Look for conservation of a particular function or annotation in the set of differentially expressed genes. GSEA Gene Set Enrichment Analysis http://www.broad.mit.edu/gsea/software/software_index.html • Look for annotations that are differentially expressed (as a group). Ex. Tour de France

  13. UIMaDS - Overview UIMaDS: a software system to provide large-scale gene expression experiment data management and analysis Commercial solutions exist, but the ability to customize analyses allows us to identify and implement to most desirable functionality for our needs. Growing Statistical Pipeline • ANOVA, t-test, GSEA, probe masking

  14. UIMaDS 2.0(Main Page)

  15. UIMaDS

  16. UIMaDS

  17. UIMaDS - Analysis

  18. UIMaDS 2.0(Analysis Result Selection)

  19. End

  20. UIMaDS 2.0(Single Analysis Result)

  21. Analysis (part 2) Association Identifying a pattern of occurrence between two independent variables. Ex. AMD and Complement Factor H

  22. Genotype-Phenotype Correlations Correlation to a clinically defined phenotype, or to an experimentally identified phenotype. • Expression • Alternative splicing • Computationally identified phenotype

  23. Collaborative Phenotype Database (CPDB) Purpose: Manage phenotypic information, both textual and image-based Facilitates the integration of phenotypic and molecular data Can help in identifying and managing phenotypic data e.g. cuticular drusen

  24. Image Data

  25. Podbielniak - the solution • Slide transport is a solved problem • Taking pictures also a solved problem

  26. CPDB Pilot Study Genome-wide Association Study for AMD • 400 AMD, 400 controls • fundus photos of retinas (10,000’s images) • patient clinical and demographic information • 500K SNP chip genotyping

  27. Acknowledgements Todd Scheetz Adam Deluca Tom Bair Hakeem Almabrazi Edwin Stone Rob Mullins Jim Folk Mike Grassi Terry Braun Thomas Casavant Abe Clark (Alcon)

  28. Pod assembly

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