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TECHNION - ISRAEL INSTITUTE OF TECHNOLOGY DEPARTMENT OF COMPUTER SCIENCE HAIFA 32000, ISRAEL מכון טכנולוגי לישראל- הטכניון הפקולטה למדעי המחשב 00333 חיפה +972-4-8294313 :'טל +972-4-8293900 :'פקס www.cs.technion.ac.il Tel.: +972-4-8294313 Fax.: +972-4-8293900 www.cs.technion.ac.il Bioinformatics Workshop Series Microarray Technology and Analysis Date & time: Monday, December 12, 2005, 10:00-13:00 Location : Seminar room (Middle floor), The Ruth and Bruce Rappaport Faculty of Medicine, Technion, Bat Galim, Haifa Please register by e-mailing your details (Name/Lab/tel.#/Faculty or Center) to Michael Shmoish <[email protected]>. Program : 10:00 - 10:10 Prof. Eddy Karnieli, MD, Director, Inst. Endocrinology, Diabetes & Metabolism, Rambam Medical Center & RB Rappaport Faculty of Medicine, Technion Dr. Michael Shmoish, COBI node manager, Computer Science Dept., Technion Welcome 10:10 – 11:00 Mr. Amos Grundwag, Affymetrix Application Support , Eisenberg Bros. Beyond Expression: New Applications of Affymetrix GeneChip Technology DNA microarrays are a well-established technology for measuring gene expression levels. Currently, microarrays designed for this purpose are biased toward known and predicted gene structures, and use relatively few probes for each gene. With the ability to shrink feature size, new families of whole-genome microarrays have been developed as an enhanced platform for genomic analysis, beyond simple gene expression profiling. Potential uses for such whole-genome arrays include analysis of alternative splicing, chromatin-immunoprecipitation studies, empirical annotation of the transcriptome, characterization of the methylome (the methylation state of the genome), polymorphism discovery and genotyping, comparative genome hybridization (CGH), and genome resequencing. This talk will review different whole-genome microarray designs, approaches and applications of the technology, including: All-Exon arrays - for exon-level expression profiling; Tiling arrays - to map sites of protein-DNA interaction or to discover novel RNA transcripts; 500k-SNP Genotyping arrays - for whole-genome association studies. 11:00 – 11:20 Coffee break 11:20 – 12:10 Dr. Ron Ophir, Bioinformatics Unit, Weizmann Institute of Science Conceptual considerations in the microarray experiments Frequently researchers who are novice to microarray find themselves in a situation where they going to spend a lot of money on a microarray experiment without knowing how to take the most of it. To help the researcher for an educated decision, we will discuss the differences between two types of microarray technologies. Issues in experimental design considering RNA amount, pooling, replicates, etc. Finally, we will give a few examples of biological questions using microarray technology. 12:10 – 13:00 Dr. Ran Elkon, Dept. of Human Genetics, Sackler School of Medicine, Tel Aviv University Analysis of gene expression microarray data using EXPANDER and SHARP EXPANDER is an integrative package for the analysis of gene expression data, designed as a 'onestop shop' tool that implements various data analysis algorithms ranging from the initial steps of normalization and filtering, through clustering and biclustering, to high-level functional enrichment analysis that points to biological processes that are active in the examined conditions, and to promoter cis-regulatory elements analysis that elucidates transcription factors that control the observed transcriptional response. EXPANDER contains supporting information that allows high-level analysis for yeast, worm, fly, rat, mouse and human. EXPANDER integrated capabilities and its built-in support of multiple organisms make it a very powerful tool for analysis of microarray data. The package is freely available for academic users at http://www.cs.tau.ac.il/~rshamir/expander. SHARP is a knowledge-base of signaling pathways that aims to assist researchers to integrate, visualize and interpret information on signaling networks derived from both focused and high-throughput studies. SHARP includes three main software components: (1) A database of specific signaling pathways, with links to literature and to web-pages on individual entities (genes, proteins, interactions) and with tools for pathway updating. (2) A tool for graphical representation of the pathways, dynamic navigation through them, flexible graphical layouts and overlay of expression data on the maps. (3) Algorithms that analyze the data and suggest new links between selected components of the network. SHARP DB is populated with extensive data on DNA damage and cell cycle-control regulations. Moreover, SHARP capabilities are generic and therefore users can utilize it to study any other signaling pathway. SHARP can be accessed at http://www.cs.tau.ac.il/~sharp/. Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R, Shiloh Y and Elkon R. (2005). EXPANDER-an integrative program suite for microarray data analysis. BMC Bioinformatics, 6, 232. This workshop is sponsored by the Institute of Endocrinology Diabetes & Metabolism, Rambam Medical Center, by Eisenberg Bros.Affymetrix' distributors in Israel, and by the Center of Knowledge for Bioinformatics Infrastructure (COBI), supported by the Ministry of Science.