Pathway and Gene Set Analysis of Microarray Data（通路和基因微阵列数据的分析）.ppt

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Pathway and Gene Set Analysis of Microarray Data（通路和基因微阵列数据的分析）.ppt

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Pathway and Gene Set Analysis of Microarray Data（通路和基因微阵列数据的分析）

26/11/2009 Bioinformatics Workshop, Brno Pathway and Gene Set Analysis of Microarray Data Claus-D. Mayer Biomathematics Statistics Scotland (BioSS) My background Biomathematics and Statististics Scotland (BioSS): An academic research group Funded by the Scottish Government Staff distributed across different biological research institutes in Scotland BioSS employs: Statisticians, Bioinformaticians, Mathematical Modellers,… I am based at (but not employed by) the Rowett Institute (Aberdeen): Research in nutrition and health Joint Aberdeen University in 2008 The early steps of a microarray study Scientific Question (biological) Study design (biological/statistical) Conducting Experiment (biological) Preprocessing/Normalising Data (statistical) Finding differentially expressed genes (statistical) A data example Lee et al (2005) compared adipose tissue (abdominal subcutaenous adipocytes) between obese and lean Pima Indians Samples were hybridised on HGu95e-Affymetrix arrays (12639 genes/probe sets) Available as GDS1498 on the GEO database We selected the male samples only 10 obese vs 9 lean The “Result” Slightly more informative results This talk will discuss some methods of how to incorporate biological knowledge into microarray analysis The type of knowledge we deal with is rather simple: We know groups/sets of genes that for example Belong to the same pathway Have a similar function Are located on the same chromosome, etc… We will assume these groupings to be given, i.e we will not discuss methods how to detect pathways, networks, gene clusters What is a pathway? No clear definition Wikipedia: “In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by chemical reactions.” These pathways describe enzymes and metabolites But often the word “pathway” is also used to describe gene regulatory networks or protein interaction networks In all cases a pathway describes a biological f