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

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(Added "Course Programme" (needs work))
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*Department: 27 BioCentrum-DTU
 
*Department: 27 BioCentrum-DTU
 
*Home Page: http://www.cbs.dtu.dk/chipcourse/
 
*Home Page: http://www.cbs.dtu.dk/chipcourse/
 +
*Course code: 27612
  
 
===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 ==
 +
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.
 +
 +
* [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.
 +
 +
 +
=== 2-Jan-2006 (Monday): <I>Introduction to microarray technology and R software</I> ===
 +
<DL>
 +
<DT>9.00-9.30 
 +
<DD>Introduction to course ([http://www.cbs.dtu.dk/~hbjorn/Teaching/course.intro.web.pdf Lecture slides])
 +
<BR>H. Bj&oslash;rn Nielsen
 +
 +
<DT>9.30-9.45 
 +
<DD>Pre-test
 +
<BR>H. Bj&oslash;rn Nielsen
 +
 +
<DT>9.45-10.30
 +
<dd>Overview over gene expression and DNA microarray technology (Chapter 1)
 +
([http://www.cbs.dtu.dk/chipcourse/Lectures/OverviewJan06.ppt Lecture slides])</dd>
 +
<DD>Jeppe S. Spicker
 +
 +
<DT>10.30-10.45
 +
<DD><I>Break</I>
 +
 +
<DT>10.45-11.45 
 +
<DD><b>Case story:</b> 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 <i>et al</i>. 2004</A>)
 +
<BR>Ulrik de Lichtenberg
 +
 +
<DT>11.45-12.15 
 +
<DD>Demonstration of microarray equipment at CBS (in groups)
 +
 +
<BR>Tim Binnewies and Thomas Jensen
 +
 +
<DT>12.15-13.00
 +
<DD><I>Lunch Break</I>
 +
 +
<DT>13.00-13.30
 +
<DD>Introduction to UNIX and R ( <A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/BasicR.pdf" target=_blank >Lecture slides</A> )
 +
<DD>Carsten Friis <BR>
 +
 +
<DT>13.30-15.15
 +
<DD>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> )
 +
<DD>Carsten Friis, Jeppe S. Spicker, Agnieszka Juncker and H. Bj&oslash;rn Nielsen<BR>
 +
 +
<DT>15.15-15.30
 +
<DD>Test of the day
 +
<DD>Jeppe S. Spicker
 +
 +
</DD>
 +
<BR>
 +
</DL>
 +
<HR>
 +
<B>Tuesday, January 3</B>
 +
<HR>
 +
<I> Preprocessing and Bioconductor</I><DL>
 +
 +
<dt>9.00-9.45</dt>
 +
<DD>Hybridization, scanning and image analysis
 +
(<A href="http://www.cbs.dtu.dk/chipcourse/scanning_and_imageanalysis.ppt" target=_blank>Lecture slides</A> )
 +
<BR>H. Bj&oslash;rn Nielsen
 +
 +
<dt>9.45-10.45</dt>
 +
<DD><font color="#003000">Project introduction - group formation </font>
 +
<BR>H. Bj&oslash;rn Nielsen
 +
 +
<dt>10.45-11.00</dt>
 +
<dd><I>Break</I></dd>
 +
 +
<dt>11.00-12.00</dt>
 +
<DD><b>Case story:</b> Disease Gene Finding, (poster)<BR>
 +
Kasper Lage Hansen
 +
 +
<DT>12.00-13.00
 +
<DD><I>Lunch Break</I>
 +
 +
<DT>13.00-13.30
 +
<DD>Introduction to Bioconductor
 +
(<A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Bioconductor.pdf" target=_blank>Lecture slides</A>)
 +
<DD>Carsten Friis
 +
 +
<DT>13.30-14.30
 +
<DD>Exercise: Introduction to Bioconductor
 +
(<A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_Bioconductor/" target=_blank>Exercise</A>)
 +
<DD>Carsten Friis, Hanni Willenbrock and Jeppe S. Spicker
 +
 +
<dt>14.30-14.45</dt>
 +
<dd><I>Break</I></dd>
 +
 +
<DT>14.45-16.15
 +
<dd><font color="#003000">Public data - available for project (1) </font>
 +
<dd>Agnieszks Junker
 +
 +
<DT>16.15-16.30
 +
<DD>Test of the day
 +
<DD>H. Bj&oslash;rn Nielsen
 +
 +
</DL>
 +
<HR>
 +
<B>Wednesday, January 4</B>
 +
<HR>
 +
<I>Data Normalization </I>
 +
<DL>
 +
 +
<DT>9.00-10.00
 +
<DD>Normalization and expression index calculation (Section 3.1-3.4) (
 +
<A href="Normalization.pdf" target=_blank>Lecture slides</A>)
 +
<BR>H. Bj&oslash;rn Nielsen
 +
 +
<DT>10.00-10.15
 +
<DD><I>Break</I>
 +
 +
<DT>10.15-12.00
 +
<dd>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>
 +
<DD>Carsten Friis, Hanni Willenbrock and Jeppe S. Spicker
 +
 +
<DT>12.00-13.00
 +
<DD><I>Lunch Break</I>
 +
 +
<DT>13.00-14.00
 +
<DD><b>Case story:</b> A key regulator of pathogen defense responses in <i>Arabidopsis</i>
 +
(<a href="Petersen_et_al.00.pdf">Petersen et al. 2000</a>)
 +
<DD>H. Bj&oslash;rn Nielsen
 +
 +
<DT>14.00-14.15
 +
<DD><I>Break</I>
 +
 +
<DT>14.15-15:00
 +
<DD><font color="#003000">Project work - problem formulation</font>
 +
 +
<DT>15.00-15.30
 +
<DD><b>Case story:</b> Epistasis by microarray
 +
<DD>H. Bjørn Nielsen
 +
 +
<DT>15.30-15.45
 +
<DD>Test of the day
 +
<DD>H. Bj&oslash;rn Nielsen
 +
 +
</DL>
 +
<HR>
 +
<B>Thursday, January 5</B>
 +
<HR>
 +
<i>Statistical analysis</i><DL>
 +
 +
<dt>9.00-10.00
 +
<dd>Statistical analysis (Section 3.5-3.6) (<A href="StatisticalAnalysis.ppt" target=_blank>Lecture slides</A>)
 +
<BR>H. Bj&oslash;rn Nielsen</dd>
 +
 +
<DT>10.00-10.15
 +
<DD><I>Coffee Break</I>
 +
 +
<DT>10.15-12.00
 +
<DD>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>)
 +
<dd>Jeppe S. Spicker, Hanni Willenbrock and Carsten Friis
 +
 +
<DT>12.00-13.00
 +
<DD><i>Lunch Break </i>
 +
 +
<DT>13.00-13.45
 +
<dd><b>Case story:</b> Regulation of the storage protein hordein C production in barley - How to reduce N-waste
 +
<DD>Michael Hansen</DD>
 +
 +
<DT>13.45-14.00
 +
<DD><I>Break</I>
 +
 +
<DT>14.00-16.00
 +
<dd><font color="#003000">Public data - available for project (Human tissue, Spike-in, Cell cycle) </font>
 +
<dd>Carsten Friis
 +
 +
<DT>16.00-16.15
 +
<DD>Test of the day
 +
<DD>H. Bj&oslash;rn Nielsen
 +
 +
</DL>
 +
<HR>
 +
<B>Friday, January 6</B>
 +
<HR>
 +
<i>Data visualization and class prediction</i><DL>
 +
 +
<DT>9.00-9.45
 +
<dd>Dimension reduction: PCA and Clustering (Chapter 4 and 5)
 +
(<a href="Cluster.lecture.v1.0.ppt">Lecture slides</a>)
 +
<dd>Agnieszka Juncker</dd>
 +
 +
<DT>9.45-10.00
 +
<DD><I>Break</I>
 +
 +
<DT>10.00-11.15
 +
<dd>Exercise: Dimension reduction: PCA and Clustering
 +
(<a href="DimentionalReduction.htm">Exercise</a>)
 +
<dd>Jeppe S. Spicker and Agnieszka Juncker</dd>
 +
 +
<DT>11.15-12.00
 +
<DD>Classification (Chapter 8)
 +
(<a href="Class.lecture.v1.1.ppt">Lecture slides</a>)</DD>
 +
<DD>Agnieszka Juncker</DD>
 +
 +
<DT>12.00-13.00
 +
<DD><i>Lunch Break </i>
 +
 +
<DT>13.00-14.00
 +
<DD><b>Case story:</b> Predicting Toxicity - An Unfinished Case Story<BR>
 +
Jeppe S. Spicker
 +
 +
<DT>14.00-14.15
 +
<DD><I>Break</I>
 +
 +
<DT>14.15-15.00
 +
<DD>Exercise: Classification, (
 +
<a href="Classification_Exercise.htm">Exercise</a>)
 +
<DD>Jeppe S. Spicker and Agnieszka Juncker
 +
 +
<DT>15.00-15.15
 +
<DD>Test of the day
 +
<DD>Agnieszka Juncker
 +
 +
</DL>
 +
<HR>
 +
<B>Monday, January 9</B>
 +
<HR>
 +
<i>Gene annotation analysis</i><DL>
 +
<DT>9.00-11.00
 +
<DD>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>)
 +
<DD>Agnieszka Juncker and  Hanni Willenbrock
 +
 +
<DT>11.00-11.15
 +
<DD><I>Break</I>
 +
 +
<DT>11.15-12.00
 +
<DD><b>Case story:</b> F.A.R.O.
 +
 +
<DT>12.00-13.00
 +
<DD><i>Lunch Break </i>
 +
 +
<DT>13.00-13.45
 +
<DD><b>Case story:</b> DNA Chip prognosis of breast cancer - a meta analysis
 +
<DD>Steen Knudsen
 +
 +
<DT>13.45-14.00
 +
<DD><I>Break</I>
 +
 +
<DT>14.00-16.00
 +
<dd><font color="#003000">Public data - available for project (Leukemia, Plant mutants,  Rosetta compendium) </font>
 +
<dd>H. Bjørn Nielsen
 +
 +
<DT>15.15-15.30
 +
<DD>Test of the day
 +
</font>
 +
<DD>Agnieszka Juncker
 +
</DL>
 +
 +
<HR>
 +
<B>Tuesday, January 10</B>
 +
<HR>
 +
<i>Integrative Biology</i><DL>
 +
 +
<Dt>9:00-11:00
 +
<DD>Integrative Biology (with <A href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_IntBiol/" target=_blank>exercise</A>)
 +
<DD>Carsten Friis
 +
 +
<Dt>11:00-12:00
 +
<DD><font color="#003000">Project work - (project outline)</font>
 +
 +
<DT>12.00-13.00
 +
<DD><i>Lunch Break </i>
 +
 +
<DT>13.00-13.45
 +
<DD>Comparative Genomic Hybridization (CGH)
 +
<DD>Hanni Willenbrock
 +
 +
<DT>13.45-14.00
 +
<DD>Test of the day
 +
<DD>Hanni Willenbrock
 +
</DD>
 +
</DL>
 +
 +
<HR>
 +
<B>Wednesday, January 11</B>
 +
<HR>
 +
<i>Project Problem Formulation</i><DL>
 +
 +
<dt> 9.00-11.00
 +
<dd>Probe design using OligoWiz 2.0 ([http://www.cbs.dtu.dk/phdcourse/cookbooks/OligoWizLectureApril2005.ppt lecture notes]<br>
 +
<a href="../dtucourse/cookbooks/raz/27803/probedesign.php" target=_blank>Exercise guide</a> &nbsp;
 +
<a href="http://www.cbs.dtu.dk/services/OligoWiz2/" target=_blank>OligoWiz 2.0 server</a>
 +
<dd>Rasmus Wernersson
 +
 +
<dt>11.00-11.15</dt>
 +
<dd><I>Break</I></dd>
 +
 +
<Dt>11.15-12.00
 +
<DD><b>Case story:</b> From genome sequence to gene expression data in Campylobacter jejuni
 +
<DD>Peter F. Hallin
 +
 +
<DT>12.00-13.00
 +
<DD><i>Lunch Break </i>
 +
 +
<Dt>13:00-14:00
 +
<DD><font color="#003000">Project work - (Deadline for Problem formulation - hand in written P.F.)</font>
 +
 +
<dt>14.00-14.15</dt>
 +
<dd><I>Break</I></dd>
 +
 +
<Dt>14:15-15:15
 +
<DD>Exercise: Reading Data into R (<a href="http://www.cbs.dtu.dk/dtucourse/cookbooks/carsten/array2006/Ex_DataIntoR/">Exercise</a>)
 +
 +
<DD>Carsten Friis
 +
 +
<DT>15.15-15.30
 +
<DD>Test of the day
 +
<DD>Rasmus Wernersson
 +
</DD>
 +
</DL>
 +
 +
<HR>
 +
<B>Thursday, January 12</B>
 +
<HR>
 +
<i>Problem Presentations</i><DL>
 +
 +
<DT>9.00-10.30
 +
<DD>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>)
 +
<DD>H. Bj&oslash;rn Nielsen and Agnieszka Juncker
 +
 +
<dt>10.30-10.45</dt>
 +
<dd><I>Break</I></dd>
 +
 +
<DT>10.45-12.00
 +
<DD><font color="#003000">Problem presentations (5min pr. group, one slide)</font>
 +
<DD>Project groups
 +
 +
<DT>12.00-13.00
 +
<DD><i>Lunch Break </i>
 +
 +
<DT>13.00-13.30
 +
<DD>course summary
 +
<DD>H. Bj&oslash;rn Nielsen
 +
 +
<DT>13.30-
 +
<DD><font color="#003000">Project work </font>
 +
 +
</DD></DL>
 +
 +
<HR>
 +
<B>Friday, January 13 - Thursday, January 19</B>
 +
<HR>
 +
<i>Project Work</i><DL>
 +
<DT>10.00-12.00
 +
<DD><font color="#003000">Office Hours - one or more Teacher(s) can be found in auditorium 51 </font>
 +
</DD></DL>
 +
 +
<HR>
 +
<B>Friday, January 20</B>
 +
<HR>
 +
<i>Poster Session</i><DL>
 +
<DT>10.00-15.00
 +
<DD><font color="#003000">Poster Session (<B>exam</B>) - In the hall infront of CBS (building 208)</font>
 +
 +
</DD></DL>
 +
 +
<HR>
 +
<B>Wednesday, January 18 - Saturday, January 21</B>
 +
<HR>
 +
<DD>Course evaluation on <a href="http://www.campusnet.dtu.dk/">CampusNet</a><br>
 +
<DD>Please, use your student number and password to login
 +
<DD>
  
 
[[Category:Academic Courses]]
 
[[Category:Academic Courses]]

Revision as of 22:37, 1 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.

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

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