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‫ מכון טכנולוגי לישראל‬- ‫הטכניון‬
‫הפקולטה למדעי המחשב‬
00333 ‫חיפה‬
+972-4-8294313 :'‫טל‬
+972-4-8293900 :'‫פקס‬
Tel.: +972-4-8294313
Fax.: +972-4-8293900
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
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
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
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
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.