DNA Microarray Analysis

Transcription

1 DNA Microarray Analysis Course # January 2009 DTU Center for Biological Sequence analysis (CBS)

2 Teachers of the course [last year] Data pre-processing Statistics Dimension Reduction Programming R, UNIX Project work Organizer

3 Teachers of the course Hanne Jarmer Associate professor Biotechnology Engineer and PhD in Bioinformatics from DTU Worked with bioinformatics and microarray data since 1999 Teaching on this course: Technology, Image analysis, Project work and exercises

4 Teachers of the course Aron C. Eklund Works as Post.doc. Master in Biology from Massachusetts Institute of Technology Worked with bioinformatics since 1999 and microarray data since 2002 Teaching on this course: Classification, Project work and Exercises

5 Teachers of the course Chris Workman Associate Professor PhD in bioinformatics from DTU Worked with bioinformatics for more than a decade - worked with microarray data since 1999 Teaching on this course: Dimension reduction, Integrative Biology, project work

6 Teachers of the course Carsten Friis Assistant professor Chemical Engineer and PhD from DTU Worked with bioinformatics since 1997 and microarray data since 2000 Teaching on this course: R, UNIX, Project work and Exercises

7 Teachers of the course H. Bjørn Nielsen Associate professor MC in Biology (KU), PhD from DTU Worked with microarray data since 1999 Teaching on this course:, Preprocessing, Statistics, Promoter analysis, Project work and Course organizer

8 Additional Teachers of the course Qiyuan Li Nicolai Juul Simon Rasmussen Rasmus Wernersson

9 Who are you the students The course has 31 students signed up 3 Batchelor students 12 Master students (1 System Biology, 11 biotek) 10 PhD students 5 guest students, 1 international

10 Learning Objectives (L.O.) for the course That the student learn A) To apply the methods for microarray analysis on gene expression data C) To manipulate simple data structures in the statistical computing environment R B) To formulate interesting hypotheses that can be addressed by gene expressions analysis

11 Content of the course Tree main tracks A) Lectures and Discussion Microarray analysis exercises B) R and UNIX exercises C) Problem formulation and project

12 The Course Tracks time schedule Intro The Pipeline Advanced Analysis Project Period Array exercises UNIX & R Basic skills in R Learning by doing Project Intro Problem Formulation Project Poster Session 5th of January 14th of January 23th of January

13 Track A: The DNA Array Analysis Pipeline Question/hypothesis Experimental Design Array design Probe design Sample Preparation Hybridization Image analysis Buy standard Chip / Array Expression Index Calculation Normalization Comparable Gene Expression Data Statistical Analysis Fit to Model (time series) Advanced Data Analysis Clustering PCA Gene Annotation Analysis Promoter Analysis Classification Meta analysis Survival analysis Regulatory Network

14 Course Program outline Monday 5th of January Introduction to technology image analysis UNIX and R Case story: Genotyping a Mutant using Microarrays Tuesday 6th of January Normalization Expression Index calculation Bioconductor (R) Wednesday 7th of January Project work initiation (group formation) Data sets for projects cdna preprocessing

15 Course Program outline Thursday 8th of January Statistics Data sets for projects (discussion 1) Case story: FARO Friday 9th of January Dimension reduction (clustering, PCA) Classification Reading data into R Monday 12th of January Gene annotation analysis (GO, KEGG) Data sets for projects (discussion 2) Case story: Drug discovery in Alzheimer Disease

16 Course Program outline Tuesday 13th of January Probe design Integrative Biology Promoter analysis Wednesday 14th of January Project work Deadline for problem formulation - hand in written P.F. Thursday 15th of January Problem presentation (10 min pr. group) 14th to 22th of January Project work Friday 23th of January Poster session (exam)

17 Course web page Course program Lecture Slides Exercises And more

18 Test of the day will you pass the day!!? Every day with lectures we have a test of the day To sum up the topics of that day To make sure the main points gets through