Introduction to Microarray Analysis

Introduction to Microarray Analysis Introduction to Microarray Analysis Uma Chandran PhD, MSIS Department of Biomedical Informatics chandranur@upmc edu 412 623 7841 12/17/08 mailto chandranur@upmc edu[.]

Introduction to Microarray Analysis Uma Chandran PhD, MSIS Department of Biomedical Informatics chandranur@upmc.edu 412-623-7841 12/17/08 My Background  Bioinformatics Analysis Service    UPCI Department of Biomedical Informatics Clinical Genomics Facility –    Runs expression, SNP and microRNA microarrays Bioinformatics tightly integrated with data analysis Expression, SNP, proteomic, integration of proteomic and genomic data Workshop Objectives  Introduction to microarray analysis    Understand general principles BRB Array Tools from NCI HSLS also offers Array Assist, Genespring GX Not an advanced analysis course – offered through DBMI and Biostatistics  Not a statistics course    Will discuss some statistical issues Should consult literature, statistician to understand methods in detail What is a microarray    Probes on chips Detect target RNA in samples High throughput    10000s of specific probes Measure global gene expression Glass beads, chips, slides Bioinformatic approaches for analysis Tumor   Measuring 10000s of data points simultaneously High dimensional data    10 Exp x 50K = 500K How to find real differences over the noise Statistical approaches Normal Bioinformatic approaches for analysis Tumor  Class Comparison   Class Discovery   Which genes are up or down in tumors v normal, untreated v treated Within the tumor samples, are there subgroups that have a specific expression profile? Class prediction, pathway analysis etc Normal Challenges in microarray analysis  Different platforms  Ilumina, Affymetrix, Agilent…    Many file types, many data formats Need to learn platform dependent methods and software required Analysis    How to get started? Which methods? Which software? Many freely available tools Some commercial How to interpret results Public databases     Many sources for public data – labs, consortia, government Publications require that data files including raw files be made public GEO – http://www.ncbi.nlm.nih.gov/ geo/ Array Express http://www.ebi.ac.uk/arrayex press/#ae-main[0] What tools to use   Gene Spring GX (HSLS) Today’s exercise using  BRB arrays tools from NCI  Excel Interface  First install R statistical package from Bioconductor  Fairly easy to use if you don’t have access to commercial tools  Analysis is robust, display and graphics are minimal  Learn concepts using BRB