EP Tutorial - part 1 v2

Gabriella Rustici (version2, 11/08/2008) Expression Profiler for Beginners – part 1 Expression Profiler (EP) is a web-based platform for gene expression data analysis. Individual components for data pre-processing, filtering, significant gene finding, clustering, visualization, between group analysis and other statistical tools are all available in EP, mostly implemented via integration with R [3]. The web-based design of EP supports data sharing and collaborative analysis in a secure environment. Developed tools are integrated with the microarray database ArrayExpress (AE) and form the exploratory analytical front-end to those data. Users can upload in EP their own data or data retrieved from the AE database. The users only need a web browser to use EP from their local PCs. You will learn about: • The basics of Expression Profiler – how to get started • How to upload data • How to transform the data • How to filter data • How to analyze the data using basic tools such as clustering and GO annotation • How to identify differentially expressed genes using t-test Contents: 1 The basics of Expression Profiler – how to get started 2 How to upload data 3 How to transform the data 4 How to filter the data 5 Clustering analysis in Expression Profiler 6 Gene Ontology annotation in Expression Profiler 7 Identification of differentially expressed genes using t-test analysis 8 How to obtain a data matrix for experiment E-MEXP-29 This ...