2005/2006 Assignment - Microarray Analysis

This exercise was set in 2005/2006 when Hugo ven den Berg was teaching the module. It uses the R programming language (available from The R Project) and a bioinformatics library called BioConductor to analyse some cystic fibrosis microarray data from the NCBI's Gene Expression Omnibus (GEO).

There is an introduction to R online (or as a PDF file ) which may be handy.

Instructions

Martin and Sam ran the workshop to go with this exercise/assignment, their instructions are online here:

You can download the instructions as a word file , and the sample R commands . Note that this little R program will not work unless all the input files are where it expects them to be.

Credits: Martin Edwards, Samuel Robson, Heather Turner, Hugo van den Berg, Helen Bird

The Assignment

The datasets you will be analysing have already been published and consequently are available in GEO. Each group (see below) has a different GEO dataset to analyse, and an associated paper to present as a seminar.

For the assessed seminars on 14th December 2005, you will be presenting the paper relevant to your dataset. For the presentations, concentrate on the biological context of the data and don't worry about the statistical methods used in the paper. Each person in the group should present an aspect of the paper for 5-10 minutes, allowing for questions, using Powerpoint.

In the written assignments, due Friday 13th January 2006, you will need to give a full analysis of the statistical methods you have chosen.

We have already assigned each paper because we needed to check the data is all available.

Project Groups

Note that access to the PDF files is restricted, you will need a Warwick account to download them.

Group One - Elina, Femi & Antonia.

Dataset: GEO dataset GDS567
6 samples, using using Affymetrix MG-U74A Mouse chip, GPL81

Related paper: Kaur S et al. 2004
Acidic duodenal pH alters gene expression in the cystic fibrosis mouse pancreas. Am J Physiol Gastrointest Liver Physiol 287:G480-G490.

Group Two - Hayley & Jon.

Dataset: GEO dataset GDS493
8 samples, using Affymetrix HG-U133A Human chip, GPL96

Related paper: Wright et al. 2004
Gene expression profile analysis of 4-phenylbutyrate treatment of IB3-1 bronchial epithelial cell line demonstrates a major influence on heat-shock proteins. Physiol Genomics 16:204-211.

Group Three - Alistair, Mosh & Zaher.

Dataset: GEO dataset GDS588
6 samples, using Affymetrix MG-U74A Mouse chip, GPL81

Related paper: Norkina O et al. 2004
Inflammation of the cystic fibrosis mouse small intestine. Am J Physiol Gastrointest Liver Physiol 286:G1032-G1041.

Group Four - Jasmine, Dan & Paul.

Dataset: GEO dataset GDS858
19 samples, using Affymetrix HG-U133A Human chip, GPL96

Related paper: Cobb LM et al. 2004
Pseudomonas aeruginosa flagellin and alginate elicit very distinct gene expression patterns in airway epithelial cells: Implications for cystic fibrosis disease. Journal of Immunology 173:5659-5670.

P.S. Peter has put a related example online: Finding differentially expressed genes and drawing heatmaps.