DNA Microarray AnalysisCourse #27612

7-27 January 2013

DTU

Center for Biological Sequence analysis (CBS)

2

Agnieszka JunkerGraduate Engineer and PhD in Bioinformatics from DTUWorked with bioinformatics and microarray data since 2000Teaching on this course: Dimension reduction, several exercises, course coordinator.

Teachersof the course

Hanne JarmerAssociate professorBiotechnology Engineer and PhD in Bioinformatics from DTUWorked with bioinformatics and microarray data since 1999

Teaching on this course: Technology, Image analysis and stat. exercises

of the course

Teachers

Aron C. EklundPost.doc.Master in Biology from Massachusetts Institute of Technology

Worked with bioinformatics since 1999 and microarray data since 2002, specializes in cancer research

Teaching on this course: Classification

of the course

Teachers

H. Bjørn Nielsen Associate professorMC in Biology (KU), PhD from DTUWorked with microarray data since 1999

Teaching on this course:, Preprocessing, Statistics, Project work and Course organizer

of the course

Teachers

Damian PlichtaKirstine BellingJens Friis-Nielsen Simon Rasmussen Chris WorkmanAgata WesolowskaKasper Nielsen

of the course

Additional Teachers

The course has 25 students signed up

5 Bachelor students12 Master students 5 PhD students 3 “åben uddannelse”

the students

Who are you

for the course

Learning Objectives (L.O.)

That the student learn

A) To apply the methods for microarray analysis on real data

C) To manipulate simple data structures in the statistical computing environment R

B)! To formulate interesting hypotheses that can be addressed by microarray data analysis

of the course

Content

Tree main tracksA) Lectures, discussions and exercises

on microarray analysis

B)! Lectures and exercises on R

C) Problem formulation and project

Project

time schedule

The Course Tracks

Intro The Pipeline Advanced Analysis

Project Intro Project

PosterSessionR Learning by doing

Array exercises

16th of January 27th of January7th of January

ProblemFormulation

Track A: The DNA Array Analysis Pipeline

Sample PreparationHybridization

Design Arrayor bye a

standard array

Experimental Design

Statistical AnalysisFit to Model (time series)

Expression IndexCalculation

Advanced Data AnalysisClustering PCA Gene Annotation Analysis Promoter Analysis

Classification Meta analysis Survival analysis Regulatory Network

ComparableGene Expression Data

Normalization

Image analysis

Question/hypothesis

NGS data

Mapping

Monday 7nd of JanuaryIntroduction to technologyimage analysisintroduction to RCase story: Cancer

Tuesday 8rd of JanuaryNormalizationExpression Index calculationMore R

Wednesday 9th of JanuaryStatistical analysisClustering and Dimension reduction

outline

Course Program

Thursday 10th of JanuaryMore StatisticsAnnotation Enrichment Analysis

Friday 11th of JanuaryClassificationIntegrative biologyProject group formation

Monday 14th of JanuaryNext Generation Sequencing (RNAseq)Project: identify problem + data set

outline

Course Program

Tuesday 15th of JanuaryGenome Wide Association Study (GWAS)Project: problem formulation

Wednesday 16th of JanuaryProject work: problem formulationDeadline for problem formulation - hand in written P.F.

Thursday 17th of JanuaryProblem presentation (10 min pr. group)

16th to 26th of JanuaryProject work

Friday 27th of JanuaryPoster session (exam)

outline

Course Program

Course web page

• Course program• Lecture Slides• Exercises• And more

www.cbs.dtu.dk/chipcourse