Introduction to Functional Analysis with IPA (UEB-UAT Bioinformatics Course - Session 4.2 - VHIR, Barcelona)

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Course: Bioinformatics for Biomedical Research (2014).
Session: 4.2- Introduction to Functional Analysis with IPA.
Statistics and Bioinformatisc Unit (UEB) & High Technology Unit (UAT) from Vall d'Hebron Research Institute (www.vhir.org), Barcelona.

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Introduction to Functional Analysis with IPA (UEB-UAT Bioinformatics Course - Session 4.2 - VHIR, Barcelona)

  1. 1. Hospital Universitari Vall d’Hebron Institut de Recerca - VHIR Institut d’Investigació Sanitària de l’Instituto de Salud Carlos III (ISCIII) Bioinformàtica per la Recerca Biomèdica http://ueb.vhir.org/2014BRB Ferran Briansó ferran.brianso@vhir.org 22/05/2014 INTRODUCTION TO FUNCTIONAL ANALYSIS
  2. 2. 1. WORKFLOW ANALYSIS EXAMPLE 2. GENE (OR WHATEVER) LIST(S) 3. FROM LISTS TO BIOLOGY 4. BENEFITS (AND DRAWBACKS) 5. BASIC EXAMPLE 6. FUNCTIONAL ANALYSIS TOOLS 7. INGENUITY PATHWAY ANALYSIS ● The Ingenuity Vision ● IPA Knowledge Base ● IPA Definitions ● Tips & Hints for Expression Analyses 1 2 3 5 6 PRESENTATION OUTLINE 4 7
  3. 3. WORKFLOW ANALYSIS EXAMPLE1 3
  4. 4. GENE (OR WHATEVER) LIST(s)2 4 2
  5. 5. 5 FROM LISTS TO BIOLOGY3 ● Classical approach for gene list analysis: one by one – Literature, databases, ... ● Problem: – Slow and tedious task, and what is worst... – Ignores possible interactions ● Alternative approach: functional analysis (aka biological significance)
  6. 6. 6 BENEFITS (AND DRAWBACKS)4 ✔ Authomatic methods for ✔ Identification of biological processes associated with experimental results. ✔ Determination/Comparison of common functions in selected groups of genes. ✔ Analisys of connections between genes, molecules and/or diseases through literature mining, in order to find relevant associations according with experimental data. ✔ Make auxiliary information more accessible ✔ Contribute to the understanding of the underlying biological phenomena ✗ Require more sofisticated software & hardware ✗ Depend on the degree of curation of the data sources
  7. 7. BASIC EXAMPLE: from genes to functions 7 5
  8. 8. BASIC EXAMPLE: from functions to pathways 8 5
  9. 9. BASIC EXAMPLE: pathways with fold change 9 5
  10. 10. FUNCTIONAL ANALYSIS TOOLS 10 6 ● Several tools deployed in the last 15 years http://estbioinfo.stat.ub.es/resources/index.html ● Direct study of gene lists – Based on GO or other BD (KEGG...)  ● fatiGO, DAVID, GSEA, Babelomics ... [SerbGO] ● Ingenuity Pathways Analysis ● Mining relationships from literature – PubMed, Scopus, HighWire, GOPubMed, … – Ingenuity Pathways Analysis ● Analysis of pathways inferred from the lists – Pathway Explorer, MappFinder, GenMapp ... – Ingenuity Pathway Analysis
  11. 11. FUNCTIONAL ANALYSIS TOOLS 11 6
  12. 12. INGENUITY PATHWAY ANALYSIS 12 7 http://www.ingenuity.com/products/ipa + Maverix (NGS, RNA-seq...) QIAGEN's IPA
  13. 13. The Ingenuity Vision 13 7
  14. 14. IPA Knowledge Base1 14 7
  15. 15. IPA Definitions7 15
  16. 16. Tips & Hints for Expression Analyses 16 7

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