Merging microarray cell synchronization experiments through curve alignment

Data

• Arabidopsis

  The raw data⁽¹⁾ is available at the TAIR website: www.arabidopsis.org

  • Aphidicolin block release: submission number ME00365
  • Sucrose starvation: submission number ME00366

  The data can be preprocessed using BioConductor.

  (1) Menges,M., Henning,L., Gruissem,W., Murray,A.H. Genome-wide gene expression in an Arabidopsis cell suspension. Plant Molecular Biology, 53, 423-442 (2003).

• Schizosaccharomyces pombe

  The preprocessed data can be downloaded from the companion website of the article of Oliva et al.⁽²⁾.

  (2) Oliva,A., Rosebrock,A., Ferrezuelo,F., Pyne,S., Chen,H., Skiena,S. The cell cycle-regulated genes of Schizosaccharomyces pombe. PLOS, 3 7, 1239-1260 (2005).

• Training sets

  The gene sets (i.e. cyclines, histones) that have been used for detemining the optimal pasting overlap and the DTW alignment can be downloaded from here cell-cycle sets.zip.

• P-values

  All the p-values used in the article can be downloaded from here p-values.

Scripts & programs

• Dynamic Time Warper

  All the dynamic time warping was done with the GenTχWarper tool, downloadable from the Computational Biology Division website.

• P-values scripts

  The MatLab scripts for the calculation for the p-values for regulation and periodicity are available upon request.