STEM is a Java program for clustering, comparing, and visualizing short time series gene expression data (eight time points or less). STEM allows researchers to identify significant temporal expression profiles and the genes associated with these profiles and to compare the behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology (GO) database and supports GO category gene enrichment analyses for sets of genes having the same temporal expression pattern. STEM also supports the ability to easily determine and visualize the behavior of genes belonging to a given GO category, identifying which temporal expression profiles were enriched for these genes.
Systems Biology Group – Carnegie Mellon University
- Linux / MacOsX / Windows
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J. Ernst, Z. Bar-Joseph.
STEM: a tool for the analysis of short time series gene expression data.
BMC Bioinformatics, 7:191, 2006.