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

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==Overview==
 
==Overview==
  
−
===Aim/objectives===
+
=== 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
 
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===
+
=== 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.
 
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.
  
−
===Remarks===
+
=== Details ===
−
 
+
* Professor: Dr. Henrik Bjørn Nielsen
−
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.
+
* Textbook: '''''[[Guide to Analysis of DNA Microarray Data]]''''', Second Edition (Paperback) — by Steen Knudsen
−
 
+
* Home Page: http://www.cbs.dtu.dk/chipcourse/
−
===Contact===
+
* Semester: 2 January 2006 — 20 January 2006
−
*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/
+
  
 
===Key words===
 
===Key words===
 
DNA Microarrays, Expression Analysis, GeneChip, Regulatory networks, classification, systems biology
 
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.
 +
 +
* [http://www.cbs.dtu.dk/phdcourse/unixguide.html Beginner's Guide to UNIX] is available on-line.
 +
* [http://cran.r-project.org/doc/manuals/R-intro.pdf An Introduction to R] is available in PDF format.
 +
* A [ftp://ftp.funet.fi/pub/mirrors/ftp.ssh.com/pub/ssh/old/SSHSecureShellClient-3.2.5.exe 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 ([http://www.cbs.dtu.dk/~hbjorn/Teaching/course.intro.web.pdf 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)([http://www.cbs.dtu.dk/chipcourse/Lectures/OverviewJan06.ppt Lecture slides])
 +
:: Jeppe S. Spicker
 +
 +
: 10.30-10.45
 +
:: ''Break''
 +
 +
: 10.45-11.45
 +
:: '''Case story''': Analysis of the cell cycle ([http://www.cbs.dtu.dk/chipcourse/cell.cycle.lecture.pdf Lecture slides],[http://www.cbs.dtu.dk/chipcourse/deLichtenberg.Bioformatics.2004.pdf de Lichtenberg <i>et al</i>. 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 programming language|R]] ([http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/BasicR.pdf Lecture slides])
 +
:: Carsten Friis
 +
 +
: 13.30-15.15
 +
:: Exercise: Introduction to UNIX and R ([http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_BasicR/ Exercise],[http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_BasicR/Ex_BasicR_Hard.php Extra exercise])
 +
:: Carsten Friis, Jeppe S. Spicker, Agnieszka Juncker and H. Bj&oslash;rn Nielsen
 +
 +
: 15.15-15.30
 +
:: Test of the day
 +
:: Jeppe S. Spicker
 +
 +
=== Preprocessing and Bioconductor ===
 +
 +
: 09.00-09.45
 +
:: Hybridization, scanning and image analysis ([http://www.cbs.dtu.dk/chipcourse/scanning_and_imageanalysis.ppt Lecture slides])
 +
:: H. Bj&oslash;rn Nielsen
 +
 +
: 09.45-10.45
 +
:: '''Project introduction - group formation'''
 +
:: H. Bj&oslash;rn 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 ([http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Bioconductor.pdf Lecture slides])
 +
:: Carsten Friis
 +
 +
: 13.30-14.30
 +
:: Exercise: Introduction to Bioconductor ([http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_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. Bj&oslash;rn Nielsen
 +
 +
=== Data Normalization ===
 +
 +
: 09.00-10.00
 +
:: Normalization and expression index calculation (Section 3.1-3.4) ([http://www.cbs.dtu.dk/chipcourse/Normalization.pdf Lecture slides])
 +
:: H. Bj&oslash;rn Nielsen
 +
 +
: 10.00-10.15
 +
:: ''Break''
 +
 +
: 10.15-12.00
 +
:: Exercise: Normalization methods and expression index calculation ([http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_Normalization/ 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'' ([http://www.cbs.dtu.dk/chipcourse/Petersen_et_al.00.pdf Petersen et al. 2000])
 +
:: H. Bj&oslash;rn 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. Bj&oslash;rn Nielsen
 +
 +
=== Statistical analysis ===
 +
 +
: 09.00-10.00
 +
:: Statistical analysis (Section 3.5-3.6) ([http://www.cbs.dtu.dk/chipcourse/StatisticalAnalysis.ppt Lecture slides])
 +
:: H. Bj&oslash;rn Nielsen
 +
 +
: 10.00-10.15
 +
:: ''Coffee Break''
 +
 +
: 10.15-12.00
 +
:: Exercise: Statistical analysis including multiple testing correction ([http://www.cbs.dtu.dk/chipcourse/statistics.html Exercise],[http://www.cbs.dtu.dk/chipcourse/data.tab data.tab], [http://www.cbs.dtu.dk/chipcourse/annotation.tab annotation.tab], [http://www.cbs.dtu.dk/chipcourse/Listeria.pdf 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. Bj&oslash;rn Nielsen
 +
 +
=== Data visualization and class prediction ===
 +
 +
: 09.00-09.45
 +
:: Dimension reduction: PCA and Clustering (Chapter 4 and 5) ([http://www.cbs.dtu.dk/chipcourse/Cluster.lecture.v1.0.ppt Lecture slides])
 +
:: Agnieszka Juncker
 +
 +
: 09.45-10.00
 +
:: ''Break''
 +
 +
: 10.00-11.15
 +
:: Exercise: [[DNA Microarray Analysis (academic course)/Dimension reduction|Dimension reduction: PCA and Clustering]] ([http://www.cbs.dtu.dk/chipcourse/DimentionalReduction.htm Exercise])
 +
:: Jeppe S. Spicker and Agnieszka Juncker
 +
 +
: 11.15-12.00
 +
:: Classification (Chapter 8) ([http://www.cbs.dtu.dk/chipcourse/Class.lecture.v1.1.ppt 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, ([http://www.cbs.dtu.dk/chipcourse/Classification_Exercise.htm 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 ([http://www.cbs.dtu.dk/chipcourse/GO.annotation.introduction.v1.2.ppt Lecture slides], [http://www.cbs.dtu.dk/chipcourse/GO_exercise_2005.htm Exercise], [http://www.cbs.dtu.dk/chipcourse/GO.solutions 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 [http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_IntBiol/ 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 ([http://www.cbs.dtu.dk/phdcourse/cookbooks/OligoWizLectureApril2005.ppt lecture notes], [http://www.cbs.dtu.dk/dtucourse/cookbooks/raz/27803/probedesign.php Exercise guide], [http://www.cbs.dtu.dk/services/OligoWiz2/ 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 ([http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_DataIntoR/ Exercise])
 +
:: Carsten Friis
 +
 +
: 15.15-15.30
 +
:: Test of the day
 +
:: Rasmus Wernersson
 +
 +
=== Problem Presentations ===
 +
 +
: 09.00-10.30
 +
:: Promoter analysis ([http://www.cbs.dtu.dk/chipcourse/cis-analysis.lecture.ppt Lecture slides], [http://www.cbs.dtu.dk/courses/thaiworkshop/exercises/cis-analysis/cis-exercise.php Exercise])
 +
:: H. Bj&oslash;rn 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. Bj&oslash;rn 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 ==
 +
* [[DNA Microarray Analysis (academic course)/Presentation|Description]]
  
 
[[Category:Academic Courses]]
 
[[Category:Academic Courses]]

Latest revision as of 00:18, 9 August 2006

Content is archived here for educational purposes only.

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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