G1DBN (version 3.1.1)

arth800line: Arabidopsis Thaliana temporal gene expression data

Description

This data set describes the temporal log2 transformed expression of 800 genes of A. thaliana during the diurnal cycle. The data are in line, that is 2 repeated measurements time series are displayed one after the other, separated by a 'NA' value. The 800 genes are a subset of the data presented in Smith et al. (2004) selected for periodicity according to the method implemented in the R package GeneCycle (http://strimmerlab.org/software/genecycle/>).

Usage

data(arth800line)

Format

matrix with 800 columns (=genes) and 23 rows (rows 1 to 11 contain the first measumement time series, row 12 contain 'NA' values and rows 13 to 23 contain the second experiment time series).

Source

The microarray 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 G1DBN library
library(G1DBN)

## load data set
data(arth800line)
id<-c(60, 141, 260, 333, 365, 424, 441, 512, 521, 578, 789, 799)

## plot first ten time series
plot(1:23,arth800line[,60],type="l",ylim=c(2,12), xlab="Time",
 ylab="Log2 transformed expression",lwd=2,
 main="Log2 transformed expression of a subset of genes of A. Thaliana")

color=1
for (i in id){
  color=color+1
  lines(1:23,arth800line[,i,],col=color,lwd=2)
}