Systems biology course: Statistical analysis of ~omics data 4th edition 8 - 11 December 2008 Wageningen, The Netherlands Organised by the Graduates School VLAG and EPS and Wageningen UR Plant Breeding 
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Background
Nowadays increasing numbers of complete genomic sequences are available and high-throughput methods have been developed to study gene expression (transcriptomics), proteins (proteomics) and metabolite levels (metabolomics). Because high-throughput methods generate large datasets, special analysis and visualisation techniques are required to extract relevant information for elucidating the function of genes, proteins and metabolites, the interactions between these molecules and the underlying regulatory mechanisms. Statistical analysis of these data is non-trivial since in many cases the number of genes/metabolites outweighs the number of samples by hundred or thousand folds.
Target group
Basic background knowledge in Cell biology, Molecular biology, Biochemistry, Statistics and Excel. Without this knowledge, it is advisable to carry out review and remedial work for these topics regarding transcriptomics, metabolomics and statistics. No programming skills will be necessary for this course. However, some experience with computers and navigating the Internet is necessary.
Course design
In order to successfully interpret experimental results generated by these high-throughput methods we will teach in this course the principles underlying processing, analysis and visualisation of large datasets derived from transcriptomics and metabolomics experiments. The emphasis will be on statistical aspects and analysis. Relevant software will be mentioned and some will be used during hands-on exercises. During the course students are provided with a syllabus, handouts, exercises and an overview of relevant literature and Internet links.
Programme topics
Day 1: Transcriptomics data processing
We will discuss the various techniques used to make transcriptome data (microarray-data) ready for analysis. The focus will be on dealing with sources of technical and biological variation in data generation (pre-processing, normalisation and experimental design). In addition, the principles of different approaches to find differentially expressed genes will be explained (fold change, t-test, ANOVA, methods that control the False Discovery Rate). Transcriptomics data processing will be exercised.
Day 2: Transcriptomics data analysis
Principles of the different approaches in transcriptomics data analysis will be explained and exercised. In addition, we will discuss statistical approaches for multivariate data analysis. For the interpretation of large data sets, these analysis methods are very often linked to visualisation techniques. Therefore data visualisation techniques will be integrated in this module (clustering, PCA). Ways of relating large numbers of genes or metabolites to phenotypic data will be discussed.
Day 3: Metabolomics data processing
Metabolomics data can be obtained using different analytical techniques. In this course we will focus on GC-MS and LC-MS. We will explain the principles of data structure and the steps that are needed to process metabolomics data for analysis (baseline extraction, peak selection, chromatogram alignment). In exercises chromatograms and MS spectra will be compared manually and processed metabolomics data will be analysed in Excel and through clustering and PCA analysis.
Day 4: Classification methods and Systems biology
After identifying mass differences, the masses need to be assigned to compounds. We will explain the paths towards compound identification. Different statistical approaches for classifying biological samples by their expression or metabolic profile will be treated, as well as cross validation procedures for estimating the quality of the classifier, and the selection of genes or metabolites useful in predicting a phenotype of interest.
Click here for the draft programme.
Course coordinators
Lecturers
Date & duration
The course will be held from 8 - 11 December 2008 (4 days).
Study load
The study load of this course is 1.4 ECTS credits.
Language
The course will be conducted in English.
Location & accommodation
Lectures will be given at:
Wageningen University
Building 352; Rooms: C90 (lectures) PC93/94 (practicals),
Arboretumlaan 4,
Wageningen
A number of rooms have been blocked for course participants at the WICC, but only until November 1st, 2008. Accommodation costs are about € 75 (single room) per night incl. breakfast, excl. tax. Participants have to book their own hotel room.
Hotel reservation is handled by WICC, Phone: +31-317-490133, http://www.hofvanwageningen.nl/.
Mention booking code: SB'08.
Contact information
More information about the course contents can be obtained from:
Dr. Chris Maliepaard (chris.maliepaard@wur.nl)
For organisational matters please contact:
Mrs. Ingeborg van Leeuwen-Bol (Ingeborg.vanLeeuwen-Bol@wur.nl)
| VLAG/EPS PhD students | € 200 |
| PhD students | € 400 |
| University staff/Non-profit | € 700 |
| Industry | € 1400 |
Cancellation may be free of charge until October 8th, 2008. After this date the charge will be 25% of the fee paid or due. Substitution may be made until the start of the course.
Registration is closed (from 17 September onwards).
For further questions, please contact Ingeborg van Leeuwen-Bol (Ingeborg.vanLeeuwen-Bol@wur.nl).