Time Series Expression Data for 800 Arabidopsis Thaliana Genes

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 (http://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 (http://affymetrix.arabidopsis.info/ 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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(GeneNet)
Loading required package: corpcor
Loading required package: longitudinal
Loading required package: fdrtool
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/GeneNet/arth800.Rd_%03d_medium.png", width=480, height=480)
> ### Name: arth800
> ### Title: Time Series Expression Data for 800 Arabidopsis Thaliana Genes
> ### Aliases: arth800 arth800.descr arth800.expr arth800.mexpr arth800.name
> ###   arth800.probe arth800.symbol
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # load GeneNet library
> library("GeneNet")
> 
> # load data set
> data(arth800)
> 
> is.longitudinal(arth800.expr)
[1] TRUE
> summary(arth800.expr)
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()'.
> 
> # plot first nine time series
> plot(arth800.expr, 1:9)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>