Transcriptomics
This course provides an introduction to Transcriptomics incorporating and using the related EBI resources and practicals, trainer-guided demonstration of when, why and how to use them. You will learn about different microarray applications, designing a microarray experiment, microarray data analysis and links to other EBI resources for microarray gene set analysis. Moreover, you will also be introduce to EnVision, an integration platform developed by Enfin Network of Excellence.
Topics include
- Microarray data storage - ArrayExpress
- Array quality metrics and normalization - Bioconductor
- Experimental design; statistics behind microarray; hypothesis testing; Introduction to limma - Bioconductor
- Overview of the principles and methods for differentially expressed genes identification: t-test; ANOVA; False Discovery Rate - Expression Profiler and Bioconductor (limma)
- Dealing with different data types (Affymetrix, Illumina)
- Looking for biological patterns in the data: Clustering; Meta analysis; Gene set analysis- Expression Profiler, Bioconductor, GO and Reactome.
- Enfin: Functional analysis of gene lists and networks
| Time | Topic |
|---|---|
| Day 1 - Mon 19 Jan 2009 | |
| 13:00 – 13:30 | Registration |
| 13:30 - 15:00 | Lecture and Hands on: ArrayExpress/Atlas (Gabriella Rustici) |
| 15:00 - 15:15 | Coffee |
| 15:15 - 17:00 | Lecture and Hands on: Expression Profiler (Gabriella Rustici) |
| 17:00 - 18:00 | Lecture and Hands on: Functional analysis of gene lists and networks using g:Profiler, GraphWeb and KEGGanim (Jury Reimand) |
| Day 2 - Tue 20 Jan 2009 | |
| 09:00 - 10:30 | Lecture: Data pre-processing (Nuno Barbosa-Morais) |
| 10:30 - 11:00 | Coffee |
| 11:00 - 12:30 | Hands on: Introduction to limma (pre-processing) (Nuno Barbosa-Morais) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 14:30 | Lecture: Experimental design (Nuno Barbosa-Morais) |
| 14:30 - 15:30 | Hands on: Introduction to limma (pre-processing) (Nuno Barbosa-Morais) |
| 15:30 - 15:45 | Coffee |
| 15:45 – 16:40 | Lecture: Statistics of differential expression (Nuno Barbosa-Morais) |
| 16:45 – 18:00 | Hands on: Introduction to limma (pre-processing) (Nuno Barbosa-Morais) |
| Day 3 - Wed 21 Jan 2009 | |
| 09:00 - 10:45 | Lecture: Linear models (Nuno Barbosa-Morais) |
| 10:45 - 11:00 | Coffee |
| 11:00 - 12:30 | Hands on: limma (differential expression) (Nuno Barbosa-Morais) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 15:00 | Hands on: limma (differential expression) (Nuno Barbosa-Morais) |
| 15:00 - 15:15 | Coffee |
| 15:15 - 16:00 | Lecture: Illumina (Mark Dunning) |
| 16:00 - 18:00 | Hands on: Illumina (Mark Dunning) |
| Day 4 - Thu 22 Jan 2009 | |
| 09:00 - 10:00 | Lecture: Affymetrix (Christina Curtis) |
| 10:00 - 10:30 | Hands on: Affymetrix (Christina Curtis) |
| 10:30 - 10:45 | Coffee |
| 10:45 - 11:45 | Hands on: Affymetrix (Christina Curtis) |
| 11:45 - 12:30 | Lecture: Clustering (Christina Curtis) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 15:30 | Lecture and Hands on: Array Quality Metrics (Audrey Kauffmann) |
| 15:30 - 15:45 | Coffee |
| 15:45 - 16:50 | Lecture and Hands on: GO (Rachel Huntley) |
| 16:50 - 18:00 | Lecture and Hands on: Reactome (David Croft) |
There is a maximum number of 30 participants. This is a residential course, without exception, and there is a fee of £450 for single or £375 sharing accommodation which includes all accommodation and food for the duration of the course (Monday 19th after lunch, course commences at 13:00 till Thursday 22nd 18:00). If accepted for this course you will have until the 12th of December to make the full payment. If we have not received payment by this date the place will be offered to another participant. The Enfin network of Excellence will be sponsoring the course dinner in one of the Cambridge Colleges.
Please note that this course is now OVERSUBSCRIBED. A few last minute places may become available which we will offer to applicants on 05 December. If you are offered one of the last minute places you must be prepared to make payment immediately by credit card.
Registration Closed.
Guest Speakers
- Nuno Barbosa-Morais, University of Cambridge
- Jury Reimand, University of Tartu, Estonia
- Christina Curtis, University of Cambridge
- Mark Dunning, Cancer Research UK
Additional help during the practicals will be provided by
- Stewart MacArthur, Cancer Research UK
- Roslin Russel, Cancer Research UK