YeastData


To catalog genes in Saccharomyces cerevisiae whose transcript levels vary periodically within the cell cycle, mRNA levels in samples from yeast cultures were synchronized in G1 phase with alpha factor arrest. After release of the alpha factor, cells were sampled every 7 minutes over a timespan of 140 minutes, during which the cells synchronously completed two cell cycles.


datasets

YeastData_alpha

The biosvd package contains functions to reduce the input
data set from the feature x assay space to the reduced
diagonalized eigenfeature x eigenassay space, with the
eigenfeatures and eigenassays unique orthonormal superpositions
of the features and assays, respectively. Results of SVD
applied to the data can subsequently be inspected based on
generated graphs, such as a heatmap of the eigenfeature x assay
matrix and a bar plot with the eigenexpression fractions of all
eigenfeatures. These graphs aid in deciding which eigenfeatures
and eigenassays to filter out (i.e., eigenfeatures representing
steady state, noise, or experimental artifacts; or when applied
to the variance in the data, eigenfeatures representing
steady-scale variance). After possible removal of steady state
expression, steady-scale variance, noise and experimental
artifacts, and after re-applying SVD to the normalized data, a
summary html report of the eigensystem is generated, containing
among others polar plots of the assays and features, a table
with the list of features sortable according to their
coordinates, radius and phase in the polar plot, and a
visualization of the data sorted according to the two selected
eigenfeatures and eigenassays with colored feature/assay
annotation information when provided. This gives a global
picture of the dynamics of expression/intensity levels, in
which individual features and assays are classified in groups
of similar regulation and function or similar cellular state
and biological phenotype.

Anneleen Daemen

biosvd

Package for high-throughput data processing, outlier detection,
noise removal and dynamic modeling

YeastData_alpha function

An ExpressionSet with gene x sample expression data, gene annotation and sample information. Expression data comprise the un-logtransformed ratio of gene expression to reference mRNA from an asynchronous yeast culture. For the samples cell cycle phase is known. For 800 cell cycle-regulated genes, the phase in which these genes reach their peak expression was determined based on published timing of the expression of known cell cycle-regulated genes.

Format

Spellman PT, Sherlock G, Zhang MQ, et al. Comprehensive identification of cell cycle-regulated genes of the Yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9, 3273-3297 (1998).

Source

To catalog genes in Saccharomyces cerevisiae whose transcript levels vary periodically within the cell cycle, mRNA levels in samples from yeast cultures were synchronized in G1 phase with alpha factor arrest. After release of the alpha factor, cells were sampled every 7 minutes over a timespan of 140 minutes, during which the cells synchronously completed two cell cycles.

YeastData_alpha: Yeast Cell Cycle Expression

Description

Usage

Arguments

Format

Source

References