Hospital Universitari Vall d’HebronInstitut 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 Briansóferran.brianso@vhir.org

22/05/2014

INTRODUCTION TO FUNCTIONAL ANALYSIS

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

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PRESENTATION OUTLINE

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WORKFLOW ANALYSIS EXAMPLE1

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GENE (OR WHATEVER) LIST(s)2

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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)

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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

BASIC EXAMPLE: from genes to functions

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BASIC EXAMPLE: from functions to pathways

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BASIC EXAMPLE: pathways with fold change

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FUNCTIONAL ANALYSIS TOOLS

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● Several tools deployed in the last 15 yearshttp://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

FUNCTIONAL ANALYSIS TOOLS

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INGENUITY PATHWAY ANALYSIS

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http://www.ingenuity.com/products/ipa

+ Maverix (NGS, RNA-seq...)

QIAGEN's IPA

The Ingenuity Vision

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IPA Knowledge Base1

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IPA Definitions7

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Tips & Hints for Expression Analyses

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