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STEM: a tool for the analysis of short time series gene expression data

Jason Ernst* and Ziv Bar-Joseph

Author affiliations

Center for Automated and Learning and Discovery, School of Computer Science, Carnegie Mellon University, 5000 Forbes Ave., Pittsburgh, PA 15213, USA

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Citation and License

BMC Bioinformatics 2006, 7:191  doi:10.1186/1471-2105-7-191

Published: 5 April 2006

Abstract

Background

Time series microarray experiments are widely used to study dynamical biological processes. Due to the cost of microarray experiments, and also in some cases the limited availability of biological material, about 80% of microarray time series experiments are short (3–8 time points). Previously short time series gene expression data has been mainly analyzed using more general gene expression analysis tools not designed for the unique challenges and opportunities inherent in short time series gene expression data.

Results

We introduce the Short Time-series Expression Miner (STEM) the first software program specifically designed for the analysis of short time series microarray gene expression data. STEM implements unique methods to cluster, compare, and visualize such data. STEM also supports efficient and statistically rigorous biological interpretations of short time series data through its integration with the Gene Ontology.

Conclusion

The unique algorithms STEM implements to cluster and compare short time series gene expression data combined with its visualization capabilities and integration with the Gene Ontology should make STEM useful in the analysis of data from a significant portion of all microarray studies. STEM is available for download for free to academic and non-profit users at http://www.cs.cmu.edu/~jernst/stem webcite.