MicroArray Unit  

Contact persons:

Dr. Shirley Horn-Saban, Head, DNA Arrays e-mail: shirley.saban@weizmann.ac.il tel: 972 8 9344435

Dr. Ron Ophir, Micro Array Analysis e-mail: ron.ophir@weizmann.ac.il tel: 972 8 9342614

Microarray technology is a simple but robust method to screen thousands of probes at once. They are mostly used to monitor differential expression by placing thousands of gene fragments on a solid surface (such as glass), and querying them with labeled RNA which was extracted from cells/tissues that need to be compared. However, microarrays can be used for other purposes as well, such as protein interactions, SNP scoring or re-sequencing by hybridization.

The microarray unit of the Weizmann institute was founded in 1998 as part of the Genome Center, when microarrays were still at a very preliminary stage world-wide. The Affymetrix GeneChip system was installed in November 1998, being the first academic setup outside the US. The spotting robot and scanner followed, and were in full capacity by mid 2000. Today the unit serves a large range of scientists using both technologies.

Databases

Expression

General Purpose Repositories

• Stanford Microarray Database - SMD, Stanford University)
• ChipDB - Whitehead, MIT
• ExpressDB - Harvard
• RAD: RNA Abundance Database - University of Pennsylvania
• Gene Expression Omnibus - GEO, NCBI
• Compendium - Rosetta

Species Specific Repositories

• Saccharomyces - Genome Database
• Stanford Microarray - Database
• Worm microarray DNA content - Database
• AFGC - Arabidopsis - Functional Genomics Consortium
• Drosophila Microarray - Databases
• Mouse Gene Expression

Single-Nucleotide Polymorphism

• Human SNP Database - Homepage
• dbSNP - Home Page

Portal and Organisations
A set of links following by a line of description

Organisations

• NHGRI Microarray Project - Home Page
• Microarrays - Their application and the standardisation of their data (EBI)
• GATC - Genetic Analysis Technology Consortium

Microarray Portals

• Papers & Links - on microarray data analysis (Rockfeller)
• Genome Chip - by Leming Shi, PhD

Gene Ontology

What is an Ontology?
From the Stanford Knowledge Systems Lab:
"An ontology is an explicit specification of some topic. For our purposes, it is a formal and declarative representation, which includes the vocabulary (or names) for referring to the terms in that subject area and the logical statements that describe what the terms are, how they are related to each other, and how they can or cannot be related to each other. Ontologies therefore provide a vocabulary for representing and communicating knowledge about some topic and a set of relationships that hold among the terms in that vocabulary."

Regulatory Pathways

• KEGG - Regulatory Pathways
• SPAD - Signal Transduction
• CSNDB - Cell Signaling Networks
• Yeast - Pathways in MIPS
• GIF_DB - Drosophila Gene Interactions
• FlyNets - Drosophila Molecular Interactions
• Interactive Fly - Drosophila Genes
• GeNet - Gene Networks Database
• HOX-Pro - Homeobox Genes Database
• Wnt - Signaling Pathway
• RegulonDB - E. coli Transcriptional Regulation
• Transpath - Gene Regulatory Pathways
• TRANSFAC - The Transcription Factor Database

Cell Location

• PSORT

Genomic Location

• GeneLoc (UDB) - The Unified Database for Human Genome Mapping

Complete Genomes and Analysis

• NCBI - Entrez Genomes Section
• PIR - Complete Genomes
• MBGD - Comparative Microbial Genome Database
• COG - Clusters of Orthologous Groups

Inegrated Gene Ontology

Human

• Gene Cards
• HUGO - The Human Genome Organisation

• Gene Ontology Consortium

For questions or suggestions please contact: bioinfo@weizmann.ac.il