Helis Academy Course: Omics data analysis through data integration - using biological pathways, networks, and linear models

Helis Academy Course: Omics data analysis through data integration - using biological pathways, networks, and linear models

General context

The first Helis Academy Omics Data Analysis course is a collaborative effort between Maastricht University and VIB in which you will learn about transcriptomics data analysis and multi-omics data integration. We will begin the course addressing how you obtain published data from data repositories and then cover basic pre-processing steps. We will continue by introducing you to molecular pathways, from what they are, to how to make your own, to how to use them in advanced omics data analysis (transcriptomics, proteomics, metabolomics) and how this compares Gene Ontology analysis. The course will continue by zooming out to utilize your pathway analysis in a broader network analysis so you can see the bigger picture. Finally, we will finish with a day to show you how to integrate Omics data sets in an unsupervised statistical way using linear models.

It is possible to register for separate workshops on different days, a detailed program can be found below. 

Afbeelding
Interreg Vlaanderen-Nederland
Software demonstrated

WikiPathways, ELIXIR Core data repositories for omics data and the Gene Ontology

PathVisio https://www.pathvisio.org/

Cytoscape: https://cytoscape.org/

Expander: http://acgt.cs.tau.ac.il/expander/

MOFA (Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets) - http://msb.embopress.org/content/14/6/e8124

Page for installing PathVisio: https://www.pathvisio.org/downloads/installation/

Page where you can download Cytoscape: https://cytoscape.org/download.html

Docker image comprising popular Omics data integration tools: https://github.com/vibbits/rocker_conda_data_integration

Trainers

Lauren Dupuis
Lauren Dupuis

Post doctoral researcher at Maastricht University in the Department of Bioinformatics BiGCaT

Martina Summer-Kutmon

Assistant professor at Maastricht University in the Department of Bioinformatics BiGCaT and the Maastricht Center for Systems Biology

Susan Steinbusch

Assistant professor at Maastricht University in the Department of Bioinformatics BiGCaT

Friederike Ehrhart

Assistant professor at Maastricht University in the Department of Bioinformatics BiGCaT

Alexander Botzki

Alexander Botzki is head of the VIB Bioinformatics Core

Contact Alexander Botzki :

Program

Below you can find a tentative schedule which will be finetuned before the event.

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Lecture: Introduction to pathways

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Lunch

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Lecture: Introduction to PathVisio and WikiPathways

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Practical: WikiPathways academy

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Break

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Practical: Draw your own pathway in PathVisio

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Wrap up (Quiz and Q&A)

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Lecture: Data repositories and data-preprocessing

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Practical: Pre-processing hands-on with ArrayAnalysis

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Lunch

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Lecture: Pathway analysis

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Practical: Pathway analysis

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Break

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Lecture: Gene Ontology Analysis

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Practical: Gene Ontology Analysis

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Wrap up (Quiz and Q&A)

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Lecture: Network Biology

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Practical: Pathways as a source for network biology

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Gene Ontology-analysis in Cytoscape

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Lunch

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Lecture and practical: Protein-Protein Interactions

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Break

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Practical: Automation demo or work on your own dataset

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Wrap up (Quiz and Q&A)

Multi Omics Integration (transcriptomics, proteomics, metabolomics)

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Introduction Multi Omics Integration

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Hands-on MOFA

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Lunch

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Hands-on MixOmics

Contact

VIB training
Tel: +32 9 244 66 11
Mail: training@vib.be