arth800: Time Series Expression Data for 800 Arabidopsis Thaliana...

In GeneNet: Modeling and Inferring Gene Networks

Description

This data set describes the temporal expression of 800 genes of A. thaliana during the diurnal cycle. The 800 genes are a subset of the data presented in Smith et al. (2004) and were selected for periodicity according to the method implemented in the R package GeneCycle (https://cran.r-project.org/package=GeneCycle).

Usage

data(arth800)

Format

arth800.expr is a longitudinal object with repetitions, and contains the log2 transformed expression data.

arth800.mexpr is a longitudinal object, and contains the mean expression levels of arth800.expr.

arth800.descr, arth800.name, arth800.probe, arth800.symbol are vectors containing additional information about each gene.

Source

The micoarray experiments were performed in the laboratory of S. Smith (Edinburgh). The data are available from the NASCArrays database under experiment reference number NASCARRAYS-60.

References

Smith et al. 2004. Diurnal changes in the transcriptom encoding enzymes of starch metabolism provide evidence for both transcriptional and posttranscriptional regulation of starch metabolism in Arabidopsis leaves. Plant Physiol. 136: 2687-2699

Examples

# load GeneNet library
library("GeneNet")

# load data set
data(arth800)

is.longitudinal(arth800.expr)
summary(arth800.expr)

# plot first nine time series
plot(arth800.expr, 1:9)

Example output

Loading required package: corpcor
Loading required package: longitudinal
Loading required package: fdrtool
[1] TRUE
Longitudinal data:
 800 variables measured at 11 different time points
 Total number of measurements per variable: 22 
 Repeated measurements: yes 

 To obtain the measurement design call 'get.time.repeats()'.

GeneNet documentation built on Nov. 15, 2021, 1:07 a.m.