Microarray facilities, databases and software

The following core facilities are available at Johns Hopkins

Core facility Location Contact
808 PCTB Francisco Martinez Murillo, PhD.
418 N Bond Street, Suite 301
Telephone: 410-955-7327; email cancerarrays@jhmi.edu
Ross Building, Room 943 Tel: 410-502-6920; email microarray@jhu.edu

Repositories of microarray data

Repository Comment
From Stanford and the University of California at Berkeley and at San Francisco
From Alvis Brazma and colleagues at the EBI
From the Whitehead Institute
At Harvard; relational database containing yeast RNA expression data.
From Biodiscovery
From Silicon Genetics
Gene Expression Omnibus from NCBI
From the Jackson Laboratory
National Cancer Institute
The University of Manchester
U. Pennsylvania
Stanford University
A listing of databases from MGED


Microarray Gene Expression Data Group - MGED The MGED group is a grass-roots movement whose goal is to facilitate the adoption of standards for DNA-array experiment annotation and data representation, as well as the introduction of standard experimental controls and data normalization methods. There are four major standardization projects being pursuing by the group:

MIAME - The formulation of the minimum information about a microarray experiment required to interpret and verify the results.
MAGE - The establishment of a data exchange format (MAGE-ML) and object model (MAGE-OM) for microarray experiments.
Ontologies - The development of ontologies for microarray experiment description and biological material (biomaterial) annotation in particular.
Normalisation - The development of recommendations regarding experimental controls and data normalization methods.

Software for microarray image analysis and data analysis (freely available to academics)

Tool Description
A suite of tools for microarray data analysis
Bioinformatics Software Solutions
Database server for microarray data
Array analysis software
Database tool for microarrays
Cluster Analysis of Gene Expression Dynamics

Commercial software packages for microarray image analysis and data analysis

Company/product Description
Statistical and data mining software
Array analysis software from Gene Network Sciences
Microarray data analysis software from Iobioninformatics
Data mining software
Data mining software
Photoretix Array Database and software
Bioinformatic products and services (SilicoCyte)

Microarray manufacturers

Company Product
Atlas arrays
DNA Arrays
Virtek ChipWriter Pro
Pan Microarrays and Oligo sets
ArrayVision; ArrayStat
Automated Cellular Imaging System (ACIS)
Data mining software
Data mining software

Links pages for information on microarrays

Links to image analysis software; data mining software; R packages for microarray data analysis; database and LIMS software

If you have any comments, suggestions or additions to this page please send them to: bioinf@kennedykrieger.org