ptest (version 1.0-8)

B2: Benchmark set B2

Description

List for yeast genes which are most likely to be periodic (the benchmark set 2 in de Lichtenberg et al. (2005)).

Usage

data(B2)

Format

A vector containg 352 genes' names.

Source

The raw data can be downloaded from http://www.cbs.dtu.dk/cellcycle/yeast_benchmark/benchmark.php.

Details

Genes whose promoters were bound (P-value below 0.01) by at least one of nine known cell cycle transcription factors in both of the Chromatin IP studies by Simon et al. (2001) and Lee et al. (2002). To obtain a benchmark set that is independent of B1, we removed all genes included in B1 (50). The resulting benchmark set, B2, consists of 352 genes of which many should be expected to be cell cycle regulated, since their promoters are associated with known stage-specific cell cycle transcription factors.

References

De Lichtenberg, U., Jensen, L. J., Fausboll, A., Jensen, T. S., Bork, P.,& Brunak, S. (2005). Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics, 21(7), 1164-1171.

Examples

data(alpha)
data(B2)
alphaB2 <- alpha[rownames(alpha)  \%in\% B2,]