DNA Microarray Analysis (academic course)

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Overview

Aim/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.

Textbook

Remarks

The evaluated exercises/projects will be done in groups and the work done by each student must be identified, so that each student can receive and individual grade.

Contact

  • Professor: Henrik Bjørn Nielsen, build. 208, room 018, (+45) 4525 2489, hbjorn@cbs.dtu.dk
  • Department: 27 BioCentrum-DTU
  • Home Page: http://www.cbs.dtu.dk/chipcourse/
  • Course code: 27612

Key words

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

Course Programme

The course will be held from January 2 - 20, 2006 (incl.)


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.


2-Jan-2006 (Monday): 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

3-Jan-2006 (Tuesday): 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

4-Jan-2006 (Wednesday): 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

5-Jan-2006 (Thursday): 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

6-Jan-2006 (Friday): 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

9-Jan-2006 (Monday): 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

10-Jan-2006 (Tuesday): 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

11-Jan-2006 (Wednesday): 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

12-Jan-2006 (Thursday): 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

13-Jan-2006 (Friday) — 19-Jan-2006 (Thursday): Project Work

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

20-Jan-2006 (Friday): Poster Session

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

18-Jan-2006 (Wednesday) — 21-Jan-2006 (Saturday)

Course evaluation on CampusNet
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Presentation

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