1 / 13

Cellular Pathway Mapping Using Gene Expression Profiles and Upstream Elements

Cellular Pathway Mapping Using Gene Expression Profiles and Upstream Elements. Presentation By: Melanie Smith. Overview. Goal: Identify Gene Function Tool: Random Forest Classification Model Summer 1: Gene Expression Profiles

winola
Download Presentation

Cellular Pathway Mapping Using Gene Expression Profiles and Upstream Elements

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Cellular Pathway Mapping Using Gene Expression Profiles and Upstream Elements Presentation By: Melanie Smith

  2. Overview • Goal: Identify Gene Function • Tool: Random Forest Classification Model • Summer 1: Gene Expression Profiles • Summer 2: Upstream Transcription Factor Binding Sites (Regulation Elements)

  3. 21 Pathways From Kyoto Encyclopedia of Genes and Genomes • Genetic Information Processing • Ribosome • Polymerases • tRNA • Proteasome • Cellular Processes • Cell Cycle • Apoptosis • Cell Adhesion • Environmental Information Processing • MAP Kinase • PI Kinase • Human Diseases • Huntington’s Disease • Metabolism • Arginine and Proline • N-glycans • Glycolysis • Oxidative Phosphorylation • TCA Cycle • Pyrimidine • Glutathione • Valine, Leucine, Isoleucine • Porphyrin • Purine • Glycerolipids

  4. Goal Outcomes • Gene Identity • Shows what genes are affected by drugs in silico • Gene Network • Shows what genes are in a target pathway • Can explain drug side effects • Regulation Elements • Target regulators of pathways for drug therapy

  5. Tool: Random Forest

  6. Summer I • Question: How Do Pathways Relate? • Approach: • Microarrays from 60 Cell Lines • Gene Expression Profiles • Random Forest and Neural Network Classification Models • ID Gene • Find Related Pathways • Build a Network

  7. Summer II • Question: How do Pathways Relate? • Approach 2 • 7,700 genes, 21 Pathways, 301 Elements • Random Forest Classification Model • ID Gene • ID Important Regulation Elements for Each Pathway

  8. Is The Model Working? • 6 Pathways Identified 50 to 90% Error • Bugs? • Genes in a pathway may not share elements • Pathways Artificially Defined • Cell Functions may overlap in regulation

  9. Some Results • Pathway: Protein Synthesis (Ribosome Genes) • Proteins that Bind to Elements • ELK 1 and 4 – promote cell proliferation and differentiation • In Ras-raf-MAPK Signaling Cascade • MZF- Myeloid Zinc Finger • Regulates c-myb • C-myb participant of • Immature liver cell proliferation • T Cell development in Thymus • TBP- TATA Binding Protein

  10. Ending The Summer

  11. Future Paths • Combine Models • Gene Expression Profiles and Upstream Elements • Add More • Methylation, Acetylation, Phosphorylation… • Outcome • A fairly accurate Gene Prediction Model

  12. Questions?

More Related