StepMiner

Java StepMiner 1.0 (Alpha) (Sept 23, 2006)
StepMiner is a new method for analyzing time course microarray data that extracts transitions between two states, up-regulated and down-regulated. For each gene, StepMiner reports the model that best matches its behavior. The models are sequences of one or two transitions. The rising or falling direction and the time of occurrence of each transition is reported.

StepMiner can be downloaded using following links. The Java source code can be obtained upon request by email (sahoo@stanford.edu or dill@cs.stanford.edu).

References:

  1. [Abstract] [Full Text] [Pubmed] Debashis Sahoo , David L. Dill , Rob Tibshirani , and Sylvia K. Plevritis . Extracting binary signals from microarray time-course data, Nucleic Acids Research Advance Access published on May 21, 2007, doi:10.1093/nar/gkm284.
  2. [Abstract] [PDF] [Pubmed] Suvarna Bhamre, Debashis Sahoo, Vincent Paton, Amritha Ragunathan, Robert Tibshirani, David L. Dill and James D. Brooks. Temporal changes in gene expression induced by sulforaphane in human prostate cancer cells. Prostate. 2009 Feb 1;69(2):181-90.
  3. [Full Text] [Pubmed] Chi-Hwa Wu, Debashis Sahoo, Constadina Arvanitis, Nicole Bradon, David L. Dill, and Dean W. Felsher. Comparative Analysis of Murine and Human Microarrays Reveals a Gene Signature Associated with the Ability of MYC to Maintain Tumorigenesis. PLoS Genetics, 4(6):e1000090, Jun 6 2008.
  4. [Abstract] [Full Text] [Pubmed] Catherine M. Shachaf, Andrew J. Gentles, Sailaja Elchuri, Debashis Sahoo, Yoav Soen, Orr Sharpe, Omar Perez, Maria Chang, Dennis Mitchel, William H. Robinson, David Dill, Garry Nolan, Sylvia K. Plevritis and Dean W. Felsher. Genomic and proteomic analysis reveals a threshold level of MYC required for tumor maintenance. Cancer Research, 68(13):5132-5142, Jul 1 2008.

Windows :
[Zip] Download StepMiner 1.0 (Alpha) for Java 1.5
[Zip] Download StepMiner 1.0 (Alpha) for Java 1.4
Unix :
[tar.gz] Download StepMiner 1.0 (Alpha) for Java 1.5
[tar.gz] Download StepMiner 1.0 (Alpha) for Java 1.4
MAC OS X :
[Zip] For MAC OS X

Click here for StepMiner tutorial.
Click here for StepMiner command line options.



Author: Debashis Sahoo
Stanford University