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.

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. 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. WORKFLOW ANALYSIS EXAMPLE1
3

4. GENE (OR WHATEVER) LIST(s)2
4
2

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
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. BASIC EXAMPLE: from genes to functions
7
5

8. BASIC EXAMPLE: from functions to pathways
8
5

9. BASIC EXAMPLE: pathways with fold change
9
5

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. FUNCTIONAL ANALYSIS TOOLS
11
6

12. INGENUITY PATHWAY ANALYSIS
12
7
http://www.ingenuity.com/products/ipa
+ Maverix (NGS, RNA-seq...)
QIAGEN's IPA

13. The Ingenuity Vision
13
7

14. IPA Knowledge Base1
14
7

15. IPA Definitions7
15

16. Tips & Hints for Expression Analyses
16
7