Handout for ISMB 2008 tutorial : ‘ Introduction to microarray analysis ’

A Tutorial Review of Microarray Data Analysis

2 Introduction 3 2.1 High troughput experiments . . . . . . . . . . . . . . . . . . . . . 4 2.2 Biological background . . . . . . . . . . . . . . . . . . . . . . . . 4 2.2.1 DNA, proteins and the central dogma . . . . . . . . . . . 4 2.2.2 Genes and protein synthesis . . . . . . . . . . . . . . . . . 5 2.2.3 Nucleic acids hybridization . . . . . . . . . . . . . . . . . 10 2.3 Microarrays . . . ...

Making Informed Choices about Microarray Data Analysis

This article describes the typical stages in the analysis of microarray data for nonspecialist researchers in systems biology and medicine. Particular attention is paid to significant data analysis issues that are commonly encountered among practitioners, some of which need wider airing. The issues addressed include experimental design, quality assessment, normalization, and summarization of mu...

Combining Semantic Relations and DNA Microarray Data for Novel Hypotheses Generation

Although microarray experiments have great potential to support progress in biomedical research, results are not easy to interpret. Information about the functions and relations of relevant genes needs to be extracted from the vast biomedical literature. A potential solution is to use computerized text analysis methods. Our proposal enhances these methods with semantic relations. We describe an...

A biologist’s introduction to support vector machines

The support vector machine (SVM) is a pattern recognition algorithm that has been used to analyze an increasing variety of complex biological data sets, including microarray expression profiles, DNA and protein sequences, protein-protein interaction networks, tandem mass spectra, etc. This tutorial describes the algorithm in a nontechnical fashion, using as an example a leukemia microarray expr...

TUTORIAL HANDOUTS for ISMB / ECCB 2009