Breast Center Biostatistics and Informatics Core

Microarray Information

Microarray Analysis and Annotation Software
Public Microarray Data Sites

Links to microarray analysis and annotation software*

Software

Link

Free or Commercial

Comment
GCOS

http://www.affymetrix.com

Commercial

 

Array Analyzer

http://www.insightful.com/

Commercial

†

PathwayAssist

http://www.ariadnegenomics.com/products/pathway.html

Commercial

††

dChip

http://www.dchip.org

Free

†††

BRB Array Tools

http://linus.nci.nih.gov/BRB-ArrayTools.html

Free

 

David Database

http://david.niaid.nih.gov/david/

Free

 

GoMiner

http://discover.nci.nih.gov/gominer/

Free

 

GenMapp

http://www.genmapp.org/

Free

 
Bioconductor http://microarrays.unife.it/bioconductor/ Free  

* Contact Anna Tsimelzon for information on who uses these packages or for access to commercial packages

† Licenses are available and restricted for use by Informatics personnel. Contact Anna Tsimelzon for information about the package.

†† Access is available through Timbuktu. Contact Brad Nugent .

††† Up to date copy of the program and associated information files are maintained on Microarray Share, contact Anna Tsimelzon for basic instructions and how to use it.

Public Microarray Data Sites

Database

Link

Gene Expression Omnibus

http://www.ncbi.nlm.nih.gov/geo/

Public data links to dChip web page

http://www.dchip.org. From there, go to Public CEL files

ArrayExpress

http://www.ebi.ac.uk/arrayexpress/

Large-Scale Gene Expression and Microarray Links and Resources

http://industry.ebi.ac.uk/~alan/MicroArray/

Website for microarray data

http://image.thelancet.com/extras/04art5032webtable.pdf

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