DNA Microarray Analysis (academic course)

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Overview

Objectives

The DNA microarray technology plays a significant role in molecular biology, systems biology and pharmaceutical research. The aim of this course is to give students a general knowledge of methods for microarray analysis as well as the ability to apply computerized analyses on gene expression data. Furthermore, it is a goal that the students learn to formulate interesting problems/questions that can be addressed by gene expressions analysis

Content

The technology behind GeneChips and cDNA arrays; normalization of data before comparison between experiments; statistical significance of changes in expression; reduction and visualization of large data matrices: PCA and clustering; reverse engineering of regulatory networks; promoter analysis and functional analysis; integration of data; case stories. Finally a poster presentation based on a problem formulated in cooperation with the teachers.

Details

Key words

DNA Microarrays, Expression Analysis, GeneChip, Regulatory networks, classification, systems biology

Course Programme

Lectures and exercises will take place at the Center for Biological Sequence Analysis at the Technical University of Denmark, building 208, auditorium 51, in Lyngby.

Introduction to microarray technology and R software

09.00-09.30
Introduction to course (Lecture slides)
H. Bjørn Nielsen
09.30-09.45
Pre-test
H. Bjørn Nielsen
9.45-10.30
Overview over gene expression and DNA microarray technology (Chapter 1)(Lecture slides)
Jeppe S. Spicker
10.30-10.45
Break
10.45-11.45
Case story: Analysis of the cell cycle (Lecture slides,de Lichtenberg et al. 2004)
Ulrik de Lichtenberg
11.45-12.15
Demonstration of microarray equipment at CBS (in groups)
Tim Binnewies and Thomas Jensen
12.15-13.00
Lunch Break
13.00-13.30
Introduction to UNIX and R (Lecture slides)
Carsten Friis
13.30-15.15
Exercise: Introduction to UNIX and R (Exercise,Extra exercise)
Carsten Friis, Jeppe S. Spicker, Agnieszka Juncker and H. Bjørn Nielsen
15.15-15.30
Test of the day
Jeppe S. Spicker

Preprocessing and Bioconductor

09.00-09.45
Hybridization, scanning and image analysis (Lecture slides)
H. Bjørn Nielsen
09.45-10.45
Project introduction - group formation
H. Bjørn Nielsen
10.45-11.00
Break
11.00-12.00
Case story: Disease Gene Finding, (poster)
Kasper Lage Hansen
12.00-13.00
Lunch Break
13.00-13.30
Introduction to Bioconductor (Lecture slides)
Carsten Friis
13.30-14.30
Exercise: Introduction to Bioconductor (Exercise)
Carsten Friis, Hanni Willenbrock and Jeppe S. Spicker
14.30-14.45
Break
14.45-16.15
Public data - available for project (1)
Agnieszks Junker
16.15-16.30
Test of the day
H. Bjørn Nielsen

Data Normalization

09.00-10.00
Normalization and expression index calculation (Section 3.1-3.4) (Lecture slides)
H. Bjørn Nielsen
10.00-10.15
Break
10.15-12.00
Exercise: Normalization methods and expression index calculation (Exercise)
Carsten Friis, Hanni Willenbrock and Jeppe S. Spicker
12.00-13.00
Lunch Break
13.00-14.00
Case story: A key regulator of pathogen defense responses in Arabidopsis (Petersen et al. 2000)
H. Bjørn Nielsen
14.00-14.15
Break
14.15-15:00
Project work - problem formulation
15.00-15.30
Case story: Epistasis by microarray
H. Bjørn Nielsen
15.30-15.45
Test of the day
H. Bjørn Nielsen

Statistical analysis

09.00-10.00
Statistical analysis (Section 3.5-3.6) (Lecture slides)
H. Bjørn Nielsen
10.00-10.15
Coffee Break
10.15-12.00
Exercise: Statistical analysis including multiple testing correction (Exercise,data.tab, annotation.tab, Lecture)
Jeppe S. Spicker, Hanni Willenbrock and Carsten Friis
12.00-13.00
Lunch Break
13.00-13.45
Case story: Regulation of the storage protein hordein C production in barley - How to reduce N-waste
Michael Hansen
13.45-14.00
Break
14.00-16.00
Public data - available for project (Human tissue, Spike-in, Cell cycle)
Carsten Friis
16.00-16.15
Test of the day
H. Bjørn Nielsen

Data visualization and class prediction

09.00-09.45
Dimension reduction: PCA and Clustering (Chapter 4 and 5) (Lecture slides)
Agnieszka Juncker
09.45-10.00
Break
10.00-11.15
Exercise: Dimension reduction: PCA and Clustering (Exercise)
Jeppe S. Spicker and Agnieszka Juncker
11.15-12.00
Classification (Chapter 8) (Lecture slides)
Agnieszka Juncker
12.00-13.00
Lunch Break
13.00-14.00
Case story: Predicting Toxicity - An Unfinished Case Story
Jeppe S. Spicker
14.00-14.15
Break
14.15-15.00
Exercise: Classification, (Exercise)
Jeppe S. Spicker and Agnieszka Juncker
15.00-15.15
Test of the day
Agnieszka Juncker

Gene annotation analysis

09.00-11.00
Gene Onthology (GO), KEGG and ChIp-chip (Lecture slides, Exercise, Solutions)
Agnieszka Juncker and Hanni Willenbrock
11.00-11.15
Break
11.15-12.00
Case story: F.A.R.O.
12.00-13.00
Lunch Break
13.00-13.45
Case story: DNA Chip prognosis of breast cancer - a meta analysis
Steen Knudsen
13.45-14.00
Break
14.00-16.00
Public data - available for project (Leukemia, Plant mutants, Rosetta compendium)
H. Bjørn Nielsen
15.15-15.30
Test of the day
Agnieszka Juncker

Integrative Biology

09:00-11:00
Integrative Biology (with exercise)
Carsten Friis
11:00-12:00
Project work - (project outline)
12.00-13.00
Lunch Break
13.00-13.45
Comparative Genomic Hybridization (CGH)
Hanni Willenbrock
13.45-14.00
Test of the day
Hanni Willenbrock

Project Problem Formulation

09.00-11.00
Probe design using OligoWiz 2.0 (lecture notes, Exercise guide, OligoWiz 2.0 server
Rasmus Wernersson
11.00-11.15
Break
11.15-12.00
Case story: From genome sequence to gene expression data in Campylobacter jejuni
Peter F. Hallin
12.00-13.00
Lunch Break
13:00-14:00
Project work - (Deadline for Problem formulation - hand in written P.F.)
14.00-14.15
Break
14:15-15:15
Exercise: Reading Data into R (Exercise)
Carsten Friis
15.15-15.30
Test of the day
Rasmus Wernersson

Problem Presentations

09.00-10.30
Promoter analysis (Lecture slides, Exercise)
H. Bjørn Nielsen and Agnieszka Juncker
10.30-10.45
Break
10.45-12.00
Problem presentations (5min pr. group, one slide)
Project groups
12.00-13.00
Lunch Break
13.00-13.30
course summary
H. Bjørn Nielsen
13.30-
Project work

Project Work

10.00-12.00
Office Hours - one or more Teacher(s) can be found in auditorium 51

Poster Session

10.00-15.00
Poster Session (exam) - In the hall infront of CBS (building 208)

Presentation

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