DNA Microarray Analysis (academic course)
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Contents
- 1 Overview
- 2 Course Programme
- 2.1 Introduction to microarray technology and R software
- 2.2 Preprocessing and Bioconductor
- 2.3 Data Normalization
- 2.4 Statistical analysis
- 2.5 Data visualization and class prediction
- 2.6 Gene annotation analysis
- 2.7 Integrative Biology
- 2.8 Project Problem Formulation
- 2.9 Problem Presentations
- 2.10 Project Work
- 2.11 Poster Session
- 3 Presentation
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
- Professor: Dr. Henrik Bjørn Nielsen
- Textbook: Guide to Analysis of DNA Microarray Data, Second Edition (Paperback) — by Steen Knudsen
- Home Page: http://www.cbs.dtu.dk/chipcourse/
- Semester: 2 January 2006 — 20 January 2006
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.
- 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.
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)
