Microarray Data Analysis
Joaquin Dopazo, Javier Santoyo and Ana Conesa
(Department of Bioinformatics and Functional Genomics Node (INB) Centro de Investigacion Principe Felipe (CIPF) 46013, Valencia, Spain)
Back for the second time, this three day training event on microarray analysis introducing new concepts of transcriptomics with next generation sequencing.
This course covers the state-of-the-art in the above mentioned topics, which are of major relevance in today's gene expression data analysis. Through sessions of theory and practical examples, students will acquire the experience necessary to address scientific questions using gene expression array datasets and solve them. Special attention will be devoted to important (although not always taken into account) aspects in microarray data analysis, such as multiple testing or functional annotation. The course is designed to be a mixture of theoretical and practical sessions. The latter will require some familiarity with the use of web-based tools and knowledge of basic notions of statistics. Practical sessions will be carried out using the GEPAS (Herrero et al., 2003, 2007; Vaquerizas et al., 2005) environment, an integrated web tool for microarray data analysis, and the Babelomics suite (Al-Shahrour et al., 2005) for functional annotation of genome-scale experiments.
Programme
Day one
10:00-13:00
Presentation and Introduction
Structure of the course. Why microarrays? Pre- and post-genomics hypothesis testing: a note of caution. Design of experiments. Data preprocessing and normalization. Unsupervised analysis (clustering). Supervised analysis (gene selection, predictors). Functional profiling.
15:00-18:00
Normalization
Getting rid of unwanted variability from sources other than the experimental conditions assayed. Methods for Affymetrix, two-color and one-color microarrays. Theory and practical exercises using GEPAS.
Day two
10:00-13:00
Gene selection
Methods for selecting genes differentially expressed among two or more experimental conditions, correlated to a continuous variable or correlated to survival time. How to deal with the multiple-testing problem. Theory and practical exercises using GEPAS.
15:00-17:00
Predictors
Gene selection in the context of class prediction. How to deal with the selection bias problem. Different methods for class prediction. Estimating the error of classification. Interpretation of confusion matrices.
17:00-18:00
Clustering
Different clustering methods: hierarchical clustering, SOM, SOTA and k-means. Pros and cons. Measures of cluster quality. Cluster visualization.
Day three
10:00-12:00
Gene Annotation Data Bases Overview
Most popular gene and protein annotation repositories be revised. These are some of the data that the Babelomics suit imports for the functional profiling of genomic experiments.
12:00-13:00 and 15:00-17:00
Functional profiling of genomic experiments
Understanding the biological roles played by the genes in the experiments. Using different types of information for the functional profiling of microarray experiments: Gene Ontology, InterPro motifs, transcription factor binding sites, gene expression in other experiments, text-mining, etc. New trends in the analysis of microarray data: testing pathway-based or function-based hypothesis. Building up Functional Annotation using Blas2GO.
References
Albertson, D.G. And Pinkel, D. Genomic microarrays in human genetic disease and cancer. Hum Mol Genet, 2003 12 Spec No 2, R145-52
Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J: BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res 2005, 33:W460-464
Herrero J, Al-Shahrour F, Diaz-Uriarte R, Mateos A, Vaquerizas JM, Santoyo J, Dopazo J: GEPAS: A web-based resource for microarray gene expression data analysis. Nucleic Acids Res 2003, 31:3461-3467.
Herrero J, Vaquerizas JM, Al-Shahrour F, Conde L, Mateos A, Diaz-Uriarte JS, Dopazo J: New challenges in gene expression data analysis and the extended GEPAS. Nucleic Acids Res 2007, 32:W485-491
Vaquerizas JM, Conde L, Yankilevich P, Cabezon A, Minguez P, Diaz-Uriarte R, Al-Shahrour F, Herrero J, Dopazo J: GEPAS, an experiment-oriented pipeline for the analysis of microarray gene expression data. Nucleic Acids Res 2005, 33:W616-620
http://bioinfo.cipf.es http://www.gepas.org http://www.babelomics.org
** PLEASE NOTE - you are requested to bring a laptop with you, as there is a limited number of machines at the NeSc Centre, therefore, some will have to use their own laptop. Please confirm that you can bring a laptop, in the "additional information" box when booking this event.**
Registration details:
Registration fees are £60; students can register for a reduced fee of £40.
Please register via the link below (bottom of page, "book this event"). Fees can be paid by either cheque, credit card or bank transfer. Please make cheques payable to “the RSE Scotland Foundation”, and send to:
Sandra Borthwick
Scottish Bioinformatics Forum
Royal Society of Edinburgh
22-26 George Street
Edinburgh
EH2 2PQ
United Kingdom
**IMPORTANT** - Registration will not be accepted until your payment has been received.
If paying by cheque - please ensure that you send your cheque asap, if your cheque is not received within 10 days you will have to register again.
If paying by bank transfer - please put your ID No. and details of the event in the transfer.
