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InBiMedDoctoralCourse 2012

UNIMIB Joint Informatics, Biology and Medicine Short Doctoral Course 2012

Registration now closed.

Pathways Analysis

Prof. Gary Bader, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada.

Dr. Daniele Merico, Molecular And Cellular Biology Informatics Core Manager, The Centre for Applied Genomics (TCAG), Toronto, Canada.

Organized by: BIMIB DISCo and BtBs (Faculty of Mathematical, Physical and Natural Sciences) and DIMET (Faculty of Medicine).


May 17 and May 18, 2012.


The course will be held in Aula U2/8a, Edificio U2, Piazzale della Scienza, Università degli Studi di Milano Bicocca.

Target audience

This workshop is geared towards biologists working with Omics data (e.g. gene expression, protein expression, molecular interactions, large-scale genetic screens and other omics data) from human and model Eukaryotic organisms who are interested in interpreting large gene lists resulting from their experiments. Concepts will be applicable to omics data from non-eukaryotic organisms, but software and demonstrations will not cover them. Prerequisite: Your own laptop computer. Minimum requirements: 1024x768 screen resolution, 1.5GHz CPU, 1GB RAM, recent versions of Windows, Mac OS X or Linux (Most computers purchased in the past 3-4 years likely meet these requirements).

Course Objective

Many research programs often slow or stall after generating a gene list. The course covers the bioinformatics concepts and tools available for annotating and determining functional enrichment of a gene list and analyzing networks. The workshop is focused on the principles and concepts required for analyzing and conducting pathway analysis on a gene list from any organism, although focus will be on human and model Eukaryotic organisms. Specifically, we will focus on 1) getting more information about a gene list, 2) finding out how a set of genes is connected, 3) discovering what's enriched in a gene list (and using it for hypothesis generation) and 4) extending or refining a gene list. An analysis flow chart will be developed throughout the course.

Course Prerequisites, Material and Requirements


  • Students are required to come with their own laptop and have Cytoscape already installed [1].
  • It is highly recommended that students follow the course with data they are interested in analyzing. E.g., if a student is looking at some particular set of gene-expression data in her/his research activity it is highly recommended to have such data at hand during the course.

Course Slides

The course slides are on the BaderLab site.

Course Outline and Preliminary Timetable

Day 1, May 17th - Gene Lists

  • 8:30 - 9:15 Registration and WiFi credential distribution.
  • 9:15 Welcome address.
  • 9:30 Module 1: Brief introduction to gene lists
    • Ice breaking session for participants (to promote networking)
    • Gene list analysis overview presenting a workflow of concepts and tools from gene list to pathway analysis
    • Where do gene lists come from?
    • Working with gene function information o Definition, sources (e.g. Gene Ontology) and issues (e.g. quality of annotation transfer, evidence codes, working with multi-functional genes)
    • Overview of pathway analysis
  • Laboratory: Practical aspects of working with gene lists
    • Workflow of tools and steps
    • Practical: review of Cytoscape tutorial
  • 10:30 - 11:00 Coffee Break
  • 11:00 Module 2: Finding over-represented pathways in gene lists
    • Over-representation analysis (ORA)
    • Use of DAVID tool Statistics for detecting over-representation e.g. hypergeometric test, GSEA
    • Multiple testing correction: Bonferroni, Benjamini-Hochberg FDR
    • Filtering Gene Ontology e.g. using evidence codes
    • Text based enrichment analysis (Wyeth Wasserman)
  • 12:30 - 14:00 Lunch
  • 14:00 Laboratory: Performing over-representation analysis
    • Workflow of tools and steps
    • Gene Set Enrichment Analysis (GSEA) and Enrichment Maps software tool
    • DAVID tool for over-representation analysis
    • Practical: Running gene enrichment tools on your gene list
  • 15:30 - 16:00 Coffee Break
  • 16:00 Module 3: Pathway and Network Analysis
    • Overview of pathway and network analysis
    • Basic network concepts
    • Types of pathway and network information

Day 2, May 18th - Networks

  • 9:30 Module 4: Network Visualization
    • Introduction to network visualization
    • Visualizing omics data on a network or pathway
  • 10:30 - 11:00 Coffee Break
  • 11:00 Laboratory: Tutorials on Cytoscape
    • Workflow of tools and steps
    • Tutorial: Cytoscape and selected plugins
  • 12:30 - 14:00 Lunch
  • 14:00 Module 5: Gene Function Prediction
    • Functional association networks and gene function prediction
    • Functional relationships, similarity space Homology based prediction Guilt-by-association
  • 15:30 - 16:00 Coffee Break
  • 16:00 Laboratory
    • Workflow of tools and steps
    • Practical: Using GeneMANIA to assess gene and gene list function
  • (TBD) Module 6: Cytoscape plugin development in Java
    • Overview and resources

Registration and More Information

Registration now closed.

The course is organized by the BIMIB Group of the Department of Informatics, Systems and Communication, in collaboration with the Department of Biotechnology and Biosciences and the the PhD Program in Translational and Molecular Medicine (DIMET) of the Università degli Studi di Milano Bicocca.

Web sites:

Please register by sending and email to joint-doctoral-course +at+ disco.unimib.it; the same address can be used to request other inquiries. There is no fee for registering.


The course has been made possible by the Regione Lombardia ASTIL program, project RetroNet, grant n. 12-4-5148000-40; U.A 053.