APO-SYS workshop on genome and transcriptome microarray data analysis, biological network analysis and pathway charting

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The Bioinformatics Unit from Institut Curie and Ron Shamir's group from Tel-Aviv University organized training workshops on microarray data analysis, biological network analysis, pathway charting, and other omics data analysis. This web page summarizes the documents and links used at these workshops. The workshop will be divided in two days:

Day 1: Polymorphisms and genome alterations: analysis of CGH and SNP array data
Philippe Hupé, Stéphane Liva, Emmanuel Barillot (Institut Curie)

Day 2: Pathway charting and expression microarray data integration
Igor Ulitskyi, Ron Shamir (Tel Aviv Univ.)
Andrei Zinovyev, Laurence Calzone, Emmanuel Barillot (Institut Curie)


SCHEDULE

Day 1: 29 April
10am        Start of workshop
                - CAPweb, a CGH and SNP array pipeline (Stéphane Liva)
                - VAMP, an interface for visualing and analysing copy number arrays (Emmanuel Barillot)
12.30       Lunch
2pm         - Scenarios of data analysis on bladder and colon cancer (Philippe Hupé)
3.30pm    Break
4pm         - Case studies (Stéphane Liva, Philippe Hupé, Emmanuel Barillot)
5pm         End of day 1
7.30pm    Dinner (optional)

Day 2: 30 April
9am          Start of day 2
                - Charting pathways with BiNoM and CellDesigner (Laurence Calzone, Andrei Zinovyev)
10.30am   Break
                - Charting pathways with BiNoM and CellDesigner (cont)
12am        Lunch
1.30pm     - Expander (45 minutes) - microarray analysis (Igor Ulitskyi)
                 - Amadeus (45 minutes) - de-novo motif finding in promoters and 3' UTRs (Igor Ulitskyi)
                 - Spike (30 minutes) - signaling pathway knowledgebase (Igor Ulitskyi)
                 - Matisse (30 minutes) - joint analysis of network and expression data (Igor Ulitskyi)
4pm          Break
4.30pm     - Hands-on session (Igor Ulitskyi)
6.30pm     End of workshop
  


Day 1: Polymorphisms and genome alterations: analysis of CGH and SNP array data


Workshop: April 29, 2008 Institut Curie (Paris).
Organizers: Institut Curie Bioinformatics Unit: Emmanuel Barillot, Philippe Hupé, Stéphane Liva, Philippe La Rosa


This workshop aims at providing the participants with the concepts and practical tools necessary for the analysis of CGH array and SNP array data in the context of cancers and constitutional disorders. The goal is both to master these approaches for fundamental research in molecular biology and for applications in clinical research or practice (diagnosis and prognosis).
>From a bioinformatics point of view, genomic DNA microarrays raise specific problems, at the level of primary data analysis (design of experiment, normalization, identification of chromosomal breakpoints and of recurrent aberrant regions) as well as for the biological interpretation of the results (classification, correlation with expression data, data integration, functional annotation, and so on). The use of bioinformatics tools must rely on a comprehensive understanding of data acquisition and of experimental biases, as well as of the assumption that underlie the modeling of this data.

Material:

Links to documents and tools used during practical course day 1:
analysis of CGH array and SNP array data in the context of cancers

CAPweb CGH array Analysis Pipeline on the WEB
--> Raw Intensity example (for CAPweb) Download Raw Intensity example
--> Genomic Position example (for CAPweb) Download Genomic Position example
--> Clinical data example (for CAPweb) Download Clinical data example
--> Transcriptome data example (for CAPweb) Download Transcriptome data example
ACTuDB ACTuDB : a database compiling the Array-CGH data of Tumors
VAMP VAMP: Visualization and Analysis of Molecular Profiles
--> Vamp data save file Download Vamp save file

Day 2: Pathway Analysis and Data Integration


Workshop: April 30, 2008 Institut Curie (Paris).
Organizers: Andrei Zinovyev (Institut Curie), Laurence Calzone (Institut Curie), Emmanuel Barillot (Institut Curie), Igor Ulitsky (Tel Aviv University), Ron Shamir (Tel Aviv University)

This workshop will introduce six software packages for drawing, analysing biological pathways and integrating data. 

The first two systems (CellDesigner and Cytoscape) recently gathered the largest user community and became standards de facto for biological pathway analysis (see this paper, for example). To adapt Cytoscape for the needs of systems biology, we developed BiNoM plugin, extending basic Cytoscape features. 

They will be presented by Andrei Zinovyev and Laurence Calzone: 

- CellDesigner (1 hour)
- BiNoM (1,5 hour)

More specifically, during this workshop we will introduce:
* Basic notions on Systems Biology Graphical Notation standard
* Basic notions on BioPAX pathway description standard
* Basic notions on Systems Biology Markup Language standard
* Basic skills with CellDesigner v4.0
* A case study for a pathway charting
* Working with BiNoM for pathway structural analysis
* Working with BiNoM for querying pathway database

The other packages will be presented by Igor Ulitsky: 

- Expander (45 minutes) - microarray analysis
- Amadeus (45 minutes) - de-novo motif finding in promoters and 3' UTRs
- Spike (30 minutes) - signaling pathway knowledgebase
- Matisse (30 minutes) - joint analysis of network and expression data

 
The following links and references can be useful in undestanding better the content of the tutorial:

  • SBGN (Systems Biology Graphical Notation) is a format for representing graphically biological interactions e.g. protein-protein interactions, gene regulatory networks, etc. http://www.sbgn.org/
  • BioPAX (Biological Pathway Exchange) is a format for storing biological data. http://www.biopax.org/
  • SBML (Systems Biology Markup Language is a format for representing models of biochemical reaction networks. http://www.sbml.org
  • BioModels: Database of numerical models: http://www.ebi.ac.uk/biomodels/


  • Session 1: CellDesigner Basic Skills

    CellDesigner is a structured diagram editor for drawing gene-regulatory and biochemical networks that uses standard formats. We will introduce the basic features of the software.

    CellDesigner offers an « easy-to-use » and standard graphical representation of a network; facilitates exchange of models developed by different groups, using a standard language (SBML: Systems Biology Markup Language); allows to annotate the reactions, proteins, genes, etc.;  proposes links to other databases (PubMed, IHOP, BioModels, KEGG, etc.); organizes a lot of information in a unique diagram; allows an exchange with other modeling tools; offers the possibility to simulate numerical models; etc

    You can find a written support here [doc] and the presentation here [ppt].

    Session 2: BiNoM Introduction

    BiNoM is a Cytoscape plugin, developed to facilitate the manipulation of biological networks represented in standard systems biology formats and to carry out studies on the network structure. BiNoM provides the user with a complete interface for the analysis of biological networks in Cytoscape environment.

    Very good tutorial on Cytoscape environment can be found in this paper from Nature Protocols

    The first version of the BiNoM software supports the following functions:

    • Import of BioPAX, SBML and CellDesigner formats
    • Export to BioPAX, SBML and CellDesigner formats after user manipulations
    • Conversion between standards (CellDesigner->BioPAX, BioPAX->SBML)
    • Full support of BioPAX information (reaction network, interaction network, pathway structure, references), concept of BioPAX index and network interfaces
    • Browsing, editing, extracting parts, merging BioPAX files with network graph interface
    • Structural analysis of the networks (strongly connected components, path and cycle analysis, network clustering, etc.)
    • Support of generating network modular view
    • BioPAX network query system: allows to work with huge BioPAX files (such as whole Reactome or NetPath)
    • Some general purpose utilities not yet implemented in Cytoscape (clipboard operations, network updating, etc.)

    You can find the presentation here [ppt].

    Session 3:  Expander (microarray analysis)
    The powerpoint presentation can be found here [ppt] and the material for hands-on session here [doc]

    Session 4:  Amadeus (de-novo motif finding in promoters and 3' UTRs)
    The powerpoint presentation can be found here [ppt].

    Session 5:  Spike (signaling pathway knowledgebase)
    The powerpoint presentation can be found here [ppt] and the material for hands-on session here [doc]

    Session 6:  Matisse (joint analysis of network and expression data)
    The powerpoint presentation can be found here [ppt] and the material for hands-on session here [doc]

    Material:

    Links to documents and tools used during practical course day 2:
    Pathway Analysis and Data Integration

    CellDesigner Drawing gene-regulatory and biochemical networks
    --> NFkB model paper Published NFkB pathway model
    --> NFkB model Download NFkB example
    Cytoscape Analysing and Visualizing Network Data 
    --> NFkB model NFkB_final.xml
    BiNoM plugin Cytoscape plug-in for manipulating and analysing biological networks
    Reactome database A curated knowledgebase of biological pathways
    --> MAPK reactome file MAPK_Reactome.owl
    --> Homosapiens reactome file homosapiens.owl
    --> Homosapiens index file homosapiens.xgmml
    Expander microarray analysis
    --> Publication on Expander EXPANDER – an integrative program suite for microarray data analysis
    Amadeus de-novo motif finding in promoters and 3' UTRs
    --> Publication on Amadeus Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets
    Spike signaling pathway knowledgebase
    --> Publication on Spike SPIKE – a database, visualization and analysis tool of cellular signaling pathways
    Matisse joint analysis of network and expression data
    --> Publication on Matisse Identification of functional modules using network topology and high-throughput data
    Contact : bioinfo | Bioinformatics Home Page : http://bioinfo.curie.fr | Institut Curie Home Page : http://www.curie.fr