Difference between revisions of "DNA Microarray Analysis (academic course)"

Revision as of 21:30, 4 January 2006

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

• Guide to Analysis of DNA Microarray Data, Second Edition (Paperback) — by Steen Knudsen

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.

• Beginner's Guide to UNIX is available on-line.
• An Introduction to R is available in PDF format.
• A ssh client program (ftp) for windows can be installed on your private computers, allowing you to remote login to the CBS computers.

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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