GSMA: Gene Set Matrix Analysis, An Automated Method for Rapid Hypothesis Testing of Gene Expression Data.
BACKGROUND
Microarray technology has become highly valuable for identifying complex global changes in gene expression patterns. The assignment of functional information to these complex patterns remains a challenging task in effectively interpreting data and correlating results from across experiments, projects and laboratories. Methods which allow the rapid and robust evaluation of multiple functional hypotheses increase the power of individual researchers to data mine gene expression data more efficiently.


RESULTS
We have developed (gene set matrix analysis) GSMA as a useful method for the rapid testing of group-wise up- or down-regulation of gene expression simultaneously for multiple lists of genes (gene sets) against entire distributions of gene expression changes (datasets) for single or multiple experiments. The utility of GSMA lies in its flexibility to rapidly poll gene sets related by known biological function or as designated solely by the end-user against large numbers of datasets simultaneously.


CONCLUSIONS
GSMA provides a simple and straightforward method for hypothesis testing in which genes are tested by groups across multiple datasets for patterns of expression enrichment.
Cheadle
Chris
C
Genomics Core, Division of Allergy and Clinical Immunology, School of Medicine, Johns Hopkins University, 5200 Eastern Avenue, Baltimore, MD 21224.
Watkins
Tonya
T
Fan
Jinshui
J
Williams
Marc A
MA
Georas
Steven
S
Hall
John
J
Rosen
Antony
A
Barnes
Kathleen C
KC