ptest (version 1.0-8)

B3: Benchmark set B3

Description

List for yeast genes which are less likely to be periodic (the benchmark set 3 in de Lichtenberg et al. (2005)).

Usage

data(B3)

Format

A vector containg 518 genes' names.

Source

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

Details

Genes annotated in MIPS (Mewes et al., 2002) as 'cell cycle and DNA processing'. From these, we removed genes annotated specifically as 'meiosis' and genes included in B1 (67), leaving 518 genes. As a large number of genes involved in the cell cycle are not subject to transcriptional regulation (not periodic), and because B1 was explicitly removed, a relatively small fraction of these genes should be expected to be periodically expressed.

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(B3)
alphaB3 <- alpha[rownames(alpha)  \%in\% B3,]