Gene Expression Analysis


Bioinformatics software and databases are essential tools for biomedical research at NIH, yet these resources are costly and out of reach for many Labs.  We provide access to a growing list of microarray analysis tools.  These include:


MSCL Analyst's Toolbox - This toolbox includes a set of scripts accessible as either a customized menu item (Windows) or as stand alone scripts (Mac) for the analysis of Affymetrix gene chip data. The scripts are run in the JMP statistical package, see below. Also available in the toolbox are GCOS database access scripts specific for Affymetrix. Please contact us to gain access to these scripts.

Affymetrix Netaffx annotation files in JMP table form.

GO-SCAN - Gene Ontology for Significant Collection of Annotations: GO-SCAN is a bioinformatics tool that selects and presents relevant Gene Ontology (GO) annotations for a gene "hit" list from an Affymetrix microarray experiment.

Links to other servers and software:

NIAID software:    DAVID - Database for Annotation, Visualization and Integrated Discovery

NIAID software:    EASE - the Expression Analysis Systematic Explorer

JMP - is a statistical discovery application. Click here for more information.


Partek Pro - A new, full-scale microarray analysis package with strong statistical analysis capabilities.

Partek Pro - Click here for more information.

In addition, the Mathematical and Statistical Computing Lab of CIT collaborates with investigators on analysis of studies involving all aspects of microarray expression analysis, especially of Affymetrix data.


Contact Peter Munson ( for more information.