Gene network reconstruction from transcriptional dynamics under kinetic model uncertainty
A case for the second derivative
Open access publication
D. R. Bickel, Z. Montazeri, P.-C. Hsieh, M. Beatty, S. J. Lawit, and N. J. Bate, “Gene network reconstruction from transcriptional dynamics under kinetic model uncertainty: A case for the second derivative,” Bioinformatics 25, 772-779 (2009).
Gene expression time course data with replication | The non-treated values serve as a reference to normalize the treated values at the same "times." The "time" in "denom" only indicates the time of the treatment sample hybridized to the same slide as the reference sample. (These are the old dual-channel, two-color microarrays.)
See the first paragraph of page 17 of the Supplement.
Dynomics is the software suite created at the University of Ottawa that implements the gene network reconstruction methods of the above paper. The source code of Dynomics has been available for download as a zip archive file from this web page since 17 February 2009. Dynomics is compatible with Windows, UNIX, Linux, and Macintosh operating systems. It requires a recent installation of R.