Home
Method
Download
Contact

  Advanced search


Complete details regarding the C. albicans strain used, cell cycle synchronization protocol and microscopic analyses can be found in Côte P. et al.


DNA microarray version
DNA microarrays were built on Candida Genome Assembly 19 (March 2004 release) but gene-lists were filtered and updated based on Assembly 21 (CGD, September 2007 release) to remove suspicious or duplicated ORFs (download data).

Bioinformatic analysis of periodic genes
Periodicity of a gene was based on 1) the sinusoidal shape of the expression modulation, 2) the period of the signal, 3) the amplitude of the periodic modulation and 4) the reproducibility of the signal across replicates. Each normalized time-course signal was processed using a modified Least-Squares Spectral Analysis (LSSA) approach. The periodic curve was used to measure the amplitude while the peak value and curvature of the LSSA spectra established the dominant period and sinusoidal shape of the signal. Individual lenient cutoff values for the amplitude, period, sinusoidal shape and variability were established. Genes that satisfied all four criteria produced an initial list of 800 that were then individually inspected. Candida genome assembly 21 (CGD, September 2007 release) was used to discard suspicious open reading frames annotated in assembly 19. Finally, 494 genes were retained as cycling.

Gene orthology group determination
Orthologous gene groups have been created using potential protein sequence paralogs within each organism combined with their closest sequence homologs in the other species. A total of 2168 orthologous gene groups, with at least one protein member in each of the four species, were constructed from published lists of interspecies orthologs. Genome sequences and annotations for C. albicans, S. cerevisiae, S. pombe and H. sapiens were obtained from the following public repositories: CGD (www.candidagenome.org), SGD (www.yeastgenome.org), the Sanger Institute (www.sanger.ac.uk/Projects/S_pombe) and Ensembl (www.ensembl.org/Homo_sapiens). Lists of orthologous genes were obtained from the Fungal Orthogroups Repository (www.broad.mit.edu/regev/orthogroups). Added to this list was the curated gene orthology provided by CGD and the Sanger Yeast_orthologous_groups. H. sapiens orthologs to S. cerevisiae and S. pombe were taken from Inparanoid (http://inparanoid.sbc.su.se). Periodic genes with their estimated peak-time and score for S. cerevisiae, S. pombe and H. sapiens were obtained from CycleBase (www.cyclebase.org).


Candida Cell Cycle database (C3db version 1.1) last update: Thu Aug 6 14:43:47 EDT 2009