DNA Microarray Analysis (academic course)

From Christoph's Personal Wiki
Revision as of 22:37, 1 January 2006 by Christoph (Talk | contribs) (Added "Course Programme" (needs work))

Jump to: navigation, search

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.

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

9.00-9.30
Introduction to course (Lecture slides)
H. Bjørn Nielsen
9.30-9.45
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 (<A href="cell.cycle.lecture.pdf" target=_blank>Lecture slides</A>, <A href="deLichtenberg.Bioformatics.2004.pdf" target=_blank>de Lichtenberg et al. 2004</A>)
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 ( <A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/BasicR.pdf" target=_blank >Lecture slides</A> )
Carsten Friis
13.30-15.15
Exercise: Introduction to UNIX and R (<A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_BasicR/" target=_blank >Exercise</A>, <A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_BasicR/Ex_BasicR_Hard.php" target=_blank >Extra exercise </A> )
Carsten Friis, Jeppe S. Spicker, Agnieszka Juncker and H. Bjørn Nielsen
15.15-15.30
Test of the day
Jeppe S. Spicker

Tuesday, January 3

Preprocessing and Bioconductor
9.00-9.45
Hybridization, scanning and image analysis (<A href="http://www.cbs.dtu.dk/chipcourse/scanning_and_imageanalysis.ppt" target=_blank>Lecture slides</A> )
H. Bjørn Nielsen
9.45-10.45
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 (<A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Bioconductor.pdf" target=_blank>Lecture slides</A>)
Carsten Friis
13.30-14.30
Exercise: Introduction to Bioconductor (<A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_Bioconductor/" target=_blank>Exercise</A>)
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

Wednesday, January 4

Data Normalization

9.00-10.00
Normalization and expression index calculation (Section 3.1-3.4) ( <A href="Normalization.pdf" target=_blank>Lecture slides</A>)
H. Bjørn Nielsen
10.00-10.15
Break
10.15-12.00
Exercise: Normalization methods and expression index calculation, (<A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_Normalization/" target=_blank>Exercise</A>) </font>
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 (<a href="Petersen_et_al.00.pdf">Petersen et al. 2000</a>)
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 </DL>

Thursday, January 5

Statistical analysis
9.00-10.00
Statistical analysis (Section 3.5-3.6) (<A href="StatisticalAnalysis.ppt" target=_blank>Lecture slides</A>)
H. Bjørn Nielsen
10.00-10.15
Coffee Break
10.15-12.00
Exercise: Statistical analysis including multiple testing correction ( <A href="http://www.cbs.dtu.dk/chipcourse/statistics.html" target=_blank>Exercise</A>, <A href="data.tab" target=_blank>data.tab</A>, <A href="annotation.tab" target=_blank>annotation.tab</A> )(<A href="Listeria.pdf" target=_blank>Lecture</A>)
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

Friday, January 6

Data visualization and class prediction
9.00-9.45
Dimension reduction: PCA and Clustering (Chapter 4 and 5) (<a href="Cluster.lecture.v1.0.ppt">Lecture slides</a>)
Agnieszka Juncker
9.45-10.00
Break
10.00-11.15
Exercise: Dimension reduction: PCA and Clustering (<a href="DimentionalReduction.htm">Exercise</a>)
Jeppe S. Spicker and Agnieszka Juncker
11.15-12.00
Classification (Chapter 8) (<a href="Class.lecture.v1.1.ppt">Lecture slides</a>)
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, ( <a href="Classification_Exercise.htm">Exercise</a>)
Jeppe S. Spicker and Agnieszka Juncker
15.00-15.15
Test of the day
Agnieszka Juncker

Monday, January 9

Gene annotation analysis
9.00-11.00
Gene Onthology (GO), KEGG and ChIp-chip (<A href="GO.annotation.introduction.v1.2.ppt" target=_blank>Lecture slides</A>, <A href="GO_exercise_2005.htm" target=_blank>Exercise</A>, <A href="GO.solutions" target=_blank>Solutions</A>)
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 </font>
Agnieszka Juncker </DL>

Tuesday, January 10

Integrative Biology
9:00-11:00
Integrative Biology (with <A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_IntBiol/" target=_blank>exercise</A>)
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

Wednesday, January 11

Project Problem Formulation
9.00-11.00
Probe design using OligoWiz 2.0 (lecture notes
<a href="../dtucourse/cookbooks/raz/27803/probedesign.php" target=_blank>Exercise guide</a>   <a href="http://www.cbs.dtu.dk/services/OligoWiz2/" target=_blank>OligoWiz 2.0 server</a>
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 (<a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_DataIntoR/">Exercise</a>)
Carsten Friis
15.15-15.30
Test of the day
Rasmus Wernersson

Thursday, January 12

Problem Presentations
9.00-10.30
Promoter analysis (<A href="cis-analysis.lecture.ppt" target=_blank>Lecture slides</A>) (<A href="http://www.cbs.dtu.dk/courses/thaiworkshop/exercises/cis-analysis/cis-exercise.php" target=_blank>Exercise</A>)
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

Friday, January 13 - Thursday, January 19

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

Friday, January 20

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

Wednesday, January 18 - Saturday, January 21

Course evaluation on <a href="http://www.campusnet.dtu.dk/">CampusNet</a>
Please, use your student number and password to login

Retrieved from "http://wiki.christophchamp.com/index.php?title=DNA_Microarray_Analysis_(academic_course)&oldid=1605"