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STEM: Short Time-series Expression Miner

Jason Ernst jernst at
Tue Jul 12 21:26:40 PDT 2005

Dear GO Friends,

I write to inform you of a new GO microarray tool - the Short Time-series
Expression Miner (STEM).  STEM is a Java program for clustering,
comparing, and visualizing short time series gene expression data (8 time
points or fewer) that is fully integrated with GO.  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 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.

The clustering algorithm which STEM implements was recently presented at
ISMB and published in Bioinformatics.  More information about STEM can be
found at

The software is freely available to academic and non-profit users.

Best regards,
Jason Ernst
Center for Automated Learning and Discovery
School of Computer Science
Carnegie Mellon University

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