Multivariate analysis of omics data with special emphasis on metabolomics
Report from the summer school can be found here
Time: June 17-21 2019
Location: Pharmacy building at University of Tromsø The Arctic University of Norway
Lecturers: Ines Heiland, Terkel Hansen, Hans Stenlund, Virginie Brun, Joseph Diab
Schedule: We start at 11 Monday morning and wrap up by 15 Friday afternoon.
Registration deadline: closed
Social: Reserve Tuesday night for a medium difficulty hike to enjoy the midnight sun in Tromsø, and Thursday evening for a BBQ dinner!
Software preparations: Download a free version of SIMCA-P software, more information will come soon.
Picture made using Vos Viewer
Program
Can be found here
Description
Multivariate data analysis is applied to complex data sets involved in Omics (transcriptomics, proteomics and metabolomics). In this practical and hands-on summer school, we will work with methods for the analysis, visualisation, and interpretation of ‘omics’ data with a special focus on metabolomics.
The course will cover the following topics.
- Metabolism: Introduction to the biochemistry of metabolic pathways
- Metabolomics: experimental methods (including an introduction into metabolite mass spectrometry), targeted and untargeted metabolomics, stable isotope labelling
- Introduction to Proteomics.
- Study design: Confirmatory vs exploratory experiments. Profiling vs finger printing.
- Multivariate analysis: Principals of (principle component analysis) PCA and (partial least square) PLS.
- Data pre-treatment techniques: scaling, transformation, missing values, etc.
- Application of PCA to detect outliers, trends and patterns in Omics data.
- Multivariate Models fitting, interpretation and visualization.
- Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) for identification of potential biomarkers.
- S-plot (one model) and SUS-plot (two models) for biomarker identification.
- Basic pathway analysis and pathway modelling.
The school is largely based on practical sessions where the students will apply multivariate analysis on their own data using R packages and/or Simca (available for 30 days free trial). In addition, students will be introduced to metaboanalyst (open access online tool for statistical, functional and integrative analysis of metabolomics data. We will furthermore give a short introduction in how to integrate omics data into pathway modelling approaches.
Target audience
PhD students (and post docs) who:
- Works with multivariate data, especially in the omics field.
- Wish to optimize their data analysis workflow.
- Wish to learn about metabolomics methodology and application is system biology.
Learning outcomes
After completion of this summer school, participants will be able to
- Understand fundamental principles of multivariate data analysis and interpretation.
- Perform statistical integration and feature selection using multivariate methodologies.
- Apply those methods to high throughput omics studies, including their own studies.
- Have a basic knowledge about methods and approaches used in metabolomics.
Prerequisites
Previous knowledge of statistical inference, probability distributions, and regression models.
NORBIS members will have priority, and will have their travel expenses covered, as usual. NORBIS post docs may apply for travel support to contact-norbis@uib.no.
Tentative program for 2019 NORBIS summer school
Monday 17th of June
| 11:30-12:00 | Welcome
Introduction to NORBIS Introduction to the summer school |
Joseph |
| 12:00-12:30 | Lunch | |
| 12:30-14:00 | What is metabolites, metabolism and metabolomics | Hans |
| 14:00-14:15 | Coffee break | |
| 14:15-16:00 | Metabolomics study design
Targeted vs untargeted metabolomics |
Hans |
| 16:00-17:00 | Poster session |
Dinner: Pizza?
Tuesday 18th of June
| 9:00-10:00 | Introduction to Mass spectrometry and signal processing | Hans |
| 10:00-11:30 | Data pre-treatment normalization, transformation
Principle component analysis PCA |
Hans |
| 11:30-12:30 | Lunch | |
| 12:30-14:00 | Detecting outliers/batch effect.
Dimension reduction |
Hans |
| 14:00-14:15 | Coffee break | |
| 14:15-17:00 | Practical session | Hans & Joseph |
Social activity: Evening hike kl. 19:30 (weather dependent)
Wednesday 19th of June
| 9:30-10:30 | Introduction to Proteomics | Jack Bruun |
| 10:30-11:30 | The application of proteomics in biomarker discovery | Virginie Brun |
| 11:30-12:30 | Lunch | |
| 12:30-14:00 | Multivariate Regression models
PLS-OPLS |
Hans |
| 14:00-14:15 | Coffee break | |
| 14:15-17:00 | Practical session | Hans & Joseph |
Visit to the proteomic and metabolomic platforms at IFA
Thursday 20th of June
| 9:00-10:00 | Introduction to system biology | Ines |
| 10:00-11:30 | Pathway analysis | Joseph |
| 11:30-12:30 | Lunch | |
| 12:30-14:00 | Pathway modelling | Ines |
| 14:00-14:15 | Coffee break | |
| 14:15-17:00 | Practical session | Hans & Joseph |
Social activity: BBQ (weather dependent)
Friday 21th of June
| 9:00-11:30 | Participants presentation | |
| 11:30-12:30 | Lunch | |
| 12:30-14:00 | Participants presentation | |
| 14:00-15:00 | QA and discussion session | |
| 15:00 | Good bye |
P.S: The program is subject to small changes.
Previous summer schools:
NORBIS summer school 2018: “Robust and reproducible practices in bioinformatics programming“, Oslo, August 6-10 2018
NORBIS summer school 2017: “Communicating research by visualisation, illustration and storytelling”, Bergen, 28 Aug – 1 Sept 2017.
NORBIS summer school 2016: “An introduction to molecular biology, bioinformatics and biostatistics”, Bergen, 13-17 June 2016.