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Introduction to DNA Microarrays: Functional Mining of Array Patterns

Introduction to DNA Microarrays: Functional Mining of Array Patterns. Michael F. Miles, M.D., Ph.D. Depts. of Pharmacology/Toxicology and Neurology and the Center for Study of Biological Complexity mfmiles@vcu.edu 225-4054. Tertiary Analysis: Connecting Function with Expression Patterns.

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Introduction to DNA Microarrays: Functional Mining of Array Patterns

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  1. Introduction to DNA Microarrays: Functional Mining of Array Patterns Michael F. Miles, M.D., Ph.D. Depts. of Pharmacology/Toxicology and Neurology and the Center for Study of Biological Complexity mfmiles@vcu.edu 225-4054

  2. Tertiary Analysis: Connecting Function with Expression Patterns • Annotation • UniGene/Swiss-Prot, SOURCE, CARS • Biased functional assessment • Functional group interrogation Manual, GenMAPP, GeneSpring • Non-biased functional queries • PubGen • MAPPFinder, DAVID/Ease, GEPAS, others • Cytoscape • Overlaying genomics and genetics • WebQTL

  3. CARS: A Curated Annotation Database Tool

  4. Non-biased (semi) Functional Group Analysis: GenMAPP

  5. Microarray Analysis of Gene Expression in Prefrontal Cortex of Schizophrenics Mirnics et al., Neuron 28:53, 2000

  6. Tertiary Analysis: Connecting Function with Expression Patterns • Annotation • UniGene/Swiss-Prot, SOURCE, CARS • Biased functional assessment • Functional group interrogation • Manual, GenMAPP, GeneSpring • Non-biased functional queries • PubGen • MAPPFinder, DAVID/Ease, GEPAS, others • Cytoscape • Overlaying genomics and genetics • WebQTL

  7. Expression Analysis Systematic Explorer -- EASE http://apps1.niaid.nih.gov/david/upload.jsp Genome Biol. 2003;4(10):R70. Epub 2003 Sep 11.

  8. EASE -- Options in Analysis

  9. Efforts to Integrate Diverse Biological Databases with Expression Information: PubGen www.PubGen.org

  10. Tertiary Analysis: Connecting Function with Expression Patterns • Annotation • UniGene/Swiss-Prot, SOURCE, CARS • Biased functional assessment • Functional group interrogation • Manual, GenMAPP, GeneSpring • Non-biased functional queries • PubGen • MAPPFinder, DAVID/Ease, GEPAS, others • Cytoscape • Overlaying genomics and genetics • WebQTL

  11. Expression of Aldh9a1 Across BxD RI Lines

  12. WebQTL Allows Definition of Genetic “Linkage” for Expression Patterns

  13. PAM eQTL on Ch1

  14. PAM: peptidylglycine alpha amidating monooxygenase • Responsible for amidation of variety of neuropeptides, including NPY • NPY associated with acute responses to ethanol and ethanol drinking behaviors

  15. Correlation of PAM Expression with Locomotor Activity

  16. Combining Behavioral and Expression QTL Analyses Locomotor activity SGK expression Multi-gene eQTL map Results courtesy of WebQTL www.webqtl.org (R. Williams, K. Manly et al.)

  17. Expression Profiling Prot-Prot Interactions BioMed Lit Relations Expression Networks Ontology HomoloGene Genetics Pharmacology Behavior

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