Build your own gene panels 2013

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Build your own gene panels 2013

  1. 1. Sample & Assay Technologies Build Your Own Gene Expression Analysis Panels George J. Quellhorst, Jr. Ph.D. Associate Director, R&D
  2. 2. Sample & Assay Technologies Agenda What Will We Discuss? Introduction Building Your Own Gene List Getting Started Increasing Coverage Knowledgebase Interactome Sources – Where are these new genes coming from? – How many & what kinds of interactions? Quality Assurance & Quality Control Final Steps Use Case Scenario Demonstrations Summary & Discussion Q&A Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012 2
  3. 3. Sample & Assay Technologies Introduction What is GNC Pro? Pathway Analysis / Systems Biology Software Integrates Multiple Bioinformatics Resources Information Authority for Life Sciences Research Takes Advantage of Our Pathway Expertise Expedite your research process Share data through exported graphs & texts Simple & easy to access, understand & use Analyze PCR Array Data – Upcoming Webinar Develop Follow-Up Experiments Choose the Right Product for Your Research Cataloged & Custom PCR Arrays – Expand seed gene list using interactome data Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012 3
  4. 4. Sample & Assay Technologies Building Your Own Gene List Getting Started Check with PCR Array Pathways First “Off-the-Shelf” Arrays Catalog Is there a title matching the biology you study? Start with a “Seed” Gene List Source: Your Own Short Gene List Pre-Loaded Pathways: – Cancer Pathways (Nature/NCI, > 500) – Signaling, Metabolic & General Pathways (KEGG & Reactome, > 200) – Genes Associated with Human Diseases (OMIM, > 4000) – Gene Ontologies (1000s) Search each one systematically Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012 4
  5. 5. Sample & Assay Technologies Building Your Own Gene List Increasing Coverage Some gene lists long enough – skip to next step Some gene lists short – more genes likely involved More genes related to “seed” gene list Expand Graph – Finds new genes with relationships to as many inputted genes as possible Get More Neighbors – Finds new genes with relationships to single selected gene Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012 5
  6. 6. Sample & Assay Technologies Knowledgebase Interactome Sources Where are these new genes coming from? Datamining Textmining Calculations/Predictions Multiple Data Sources – One Platform Systematic Quality Control by Biological Scientists Powerful Text-Mining Algorithm & Database Processes biomedical publications Gene A – Verb – Gene B High accuracy & sensitivity Public & Licensed Omics Resources Datamined Nature / NCI Pathway Interaction Database Gemma ProLinks HPRD Tissue-Specific Gene Expression BioGPS (GNF), U Tokyo, HUGE Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012 6
  7. 7. Sample & Assay Technologies Knowledgebase Depth How Many & What Kinds of Interactions? Unique Genes Source Unique Relationships Total Relationships Text-Mined Data 6,384 36,283 97,795 Data-Mined Chemical Modifications 1,291 2,354 2,354 Third Party Protein Interactions 8,433 32,805 32,805 Data-Mined Co-Expression Data 8,526 216,104 216,267 Protein-Protein Interaction Predictions 8,152 43,364 43,364 Transcription Factor Regulation Predictions 13,684 122,700 122,700 TOTAL 20,116 448,255 515,285 Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012 7
  8. 8. Sample & Assay Technologies Building Your Own Gene List Quality Assurance & Quality Control – Final Steps Verify Interactions Click lines connecting genes – Displays evidence for relationship Not convinced? – Delete Gene remove individual genes – Helps narrow down longer gene lists Are Genes Expressed in Your Model System? View Tissue Specific Expression Export Genes Ready for submission as a Custom Gene List Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012 8
  9. 9. Sample & Assay Technologies Use Case Scenario Demonstrations Let’s see this in action Human Diseases Schizophrenia Polycystic Kidney Disease Metastatic Melanoma Glaucoma Cancer Pathways Complement Calmodulin General Pathways Rho GTPases Gene Ontologies AMPK Signaling Your Biology of Interest Type your ideas into “Questions” box – Webinar right-hand navigation bar Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012 9
  10. 10. Sample & Assay Technologies Summary & Conclusions Build Your Own Gene List Today OR Let Us Help Start Biological Search Term OR Short Gene List Expand Expand Graph & Get More Neighbors Verify Evidence for Interactions, Tissue Specific Expression Finalize Export Genes & Order Custom Content Generation Services FREE with purchase of Custom PCR Array Expert Biological Content Development Scientists Use This Process & Other Sophisticated Resources Your Biology -> Best Possible Gene List Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012 10
  11. 11. Sample & Assay Technologies Questions? Resources to Further Help You GNC Pro Related Questions: Ask Now OR Email Technical Support at support@SABiosciences.com Webinar Related Questions: Email QIAWEBINARS@QIAGEN.COM Saved PDF Slides & Recorded Sessions Alternative Times New Topics You Want to See Build Your Own Gene Expression Analysis Panels, Webinar, Tuesday, October 16, 2012 11
  12. 12. Sample & Assay Technologies Build Your Own Gene Expression Analysis Panels George J. Quellhorst, Jr. Ph.D. Associate Director, R&D

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