DNA Microarray Analysis (academic course) - Revision history

Christoph at 00:18, 9 August 2006

2006-08-09T00:18:46Z

Christoph: +FairUse

2006-05-25T23:36:02Z

+FairUse

Christoph: Added "Presentation" section

2006-01-19T20:24:22Z

Added "Presentation" section

Christoph: /* 6-Jan-2006 (Friday): ''Data visualization and class prediction'' */ link

2006-01-06T09:32:36Z

‎6-Jan-2006 (Friday): ''Data visualization and class prediction'': link

Christoph: Added "Guide to Analysis of DNA Microarray Data" texbook

2006-01-04T21:30:52Z

Added "Guide to Analysis of DNA Microarray Data" texbook

Christoph: /* Course Programme */ major format changes

2006-01-02T15:48:46Z

‎Course Programme: major format changes

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Christoph: Added "Course Programme" (needs work)

2006-01-01T22:37:08Z

Added "Course Programme" (needs work)

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Christoph: Started article

2005-12-23T00:41:10Z

Started article

New page

==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/

===Key words===
DNA Microarrays, Expression Analysis, GeneChip, Regulatory networks, classification, systems biology

[[Category:Academic Courses]]

@@ Line 2: / Line 2: @@
 ==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
-===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.
-=== Textbook ===
+=== Details ===
+* Professor: Dr. Henrik Bjørn Nielsen
-* '''''[[Guide to Analysis of DNA Microarray Data]]''''', Second Edition (Paperback) &mdash; by Steen Knudsen
+* Textbook: '''''[[Guide to Analysis of DNA Microarray Data]]''''', Second Edition (Paperback) &mdash; by Steen Knudsen
 * Home Page: http://www.cbs.dtu.dk/chipcourse/
-===Remarks===
+* Semester: 2 January 2006 &mdash; 20 January 2006
-−
-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===
@@ Line 28: / Line 20: @@
 == 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.
@@ Line 37: / Line 26: @@
 * 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 ===
-=== 2-Jan-2006 (Monday): ''Introduction to microarray technology and R software'' ===
 : 09.00-09.30
@@ Line 78: / Line 66: @@
 :: Jeppe S. Spicker
-=== 3-Jan-2006 (Tuesday): ''Preprocessing and Bioconductor'' ===
+=== Preprocessing and Bioconductor ===
 : 09.00-09.45
@@ Line 117: / Line 105: @@
 :: H. Bj&oslash;rn Nielsen
-=== 4-Jan-2006 (Wednesday): ''Data Normalization'' ===
+=== Data Normalization ===
 : 09.00-10.00
@@ Line 151: / Line 139: @@
 :: H. Bj&oslash;rn Nielsen
-=== 5-Jan-2006 (Thursday): ''Statistical analysis'' ===
+=== Statistical analysis ===
 : 09.00-10.00
@@ Line 182: / Line 170: @@
 :: H. Bj&oslash;rn Nielsen
-=== 6-Jan-2006 (Friday): ''Data visualization and class prediction'' ===
+=== Data visualization and class prediction ===
 : 09.00-09.45
@@ Line 217: / Line 205: @@
 :: Agnieszka Juncker
-=== 9-Jan-2006 (Monday): ''Gene annotation analysis'' ===
+=== Gene annotation analysis ===
 : 09.00-11.00
@@ Line 247: / Line 235: @@
 :: Agnieszka Juncker
-=== 10-Jan-2006 (Tuesday): ''Integrative Biology'' ===
+=== Integrative Biology ===
 : 09:00-11:00
@@ Line 267: / Line 255: @@
 :: Hanni Willenbrock
-=== 11-Jan-2006 (Wednesday): ''Project Problem Formulation'' ===
+=== Project Problem Formulation ===
 : 09.00-11.00
@@ Line 297: / Line 285: @@
 :: Rasmus Wernersson
-=== 12-Jan-2006 (Thursday): ''Problem Presentations'' ===
+=== Problem Presentations ===
 : 09.00-10.30
@@ Line 320: / Line 308: @@
 :: '''Project work'''
-=== 13-Jan-2006 (Friday) &mdash; 19-Jan-2006 (Thursday): ''Project Work'' ===
+=== 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'' ===
+=== Poster Session ===
 : 10.00-15.00
 :: '''Poster Session (exam)''' - In the hall infront of CBS (building 208)
 == Presentation ==

← Older revision		Revision as of 23:36, 25 May 2006
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		+	{{FairUse}}
	==Overview==		==Overview==

@@ Line 333: / Line 333: @@
 :: Course evaluation on [http://www.campusnet.dtu.dk/ CampusNet]
 :: Please, use your student number and password to login
 [[Category:Academic Courses]]

@@ Line 191: / Line 191: @@
 : 10.00-11.15
-:: Exercise: Dimension reduction: PCA and Clustering ([http://www.cbs.dtu.dk/chipcourse/DimentionalReduction.htm Exercise])
+:: 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

← Older revision		Revision as of 21:30, 4 January 2006
Line 8:		Line 8:

	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.
		+
		+	=== Textbook ===
		+
		+	* '''''[[Guide to Analysis of DNA Microarray Data]]''''', Second Edition (Paperback) — by Steen Knudsen

	===Remarks===		===Remarks===