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Identification of biological themes in microarray data from a mouse heart development time series using GeneSifter

Microarray Platform: Affymetrix® GeneChip® Murine Genome U74A

Reference: http://www.cardiogenomics.org
The data used in this analysis was obtained from the CardioGenomics PGA (Genomics of Cardiovascular Development, Adaptation, and Remodeling. NHLBI Program for Genomic Applications, Harvard Medical School. May 2004.)

Abstract:
Microarray technology allows researchers to take a genome-wide approach to studying the complex regulatory mechanisms underlying cardiac development. In this study from the CardioGenomic PGA, changes in cardiac gene expression were monitored from the E12 stage of embryonic development through 1 year old. Ventricular tissue from wildtype FVB mice was hybridized to the Affymetrix® GeneChip® Mouse Genome U74A array. Utilizing ANOVA analysis followed by the false discovery rate method of Benjamini and Hochberg, 1513 genes were identified that show significant differential regulation across the time series. These genes could be clustered into two groups using PAM; one cluster shows up-regulation of genes across the time series, and the other cluster exhibits down-regulation. Applying z-score analysis to the gene ontologies associated with the genes in each cluster identified distinct biological themes in each cluster. In the cluster of down-regulated genes, mitotic cell cycle genes were significantly over-represented, while in the up-regulated cluster, genes associated with immune response and energy pathways were over-represented.

Scientific analysis of the dataset:

Analysis Summary:	[ pdf ]
Step by Step tutorial:	[ pdf ]
WebEx presentation:	[ watch ]