phytophthora: Gene Expression Data for Tomato Plants Inoculated with...

In acde: Artificial Components Detection of Differentially Expressed Genes

Description

Gene expression data for 16 tomato plants (line IL6-2) in field conditions. 8 of these plants were inoculated with Phytophthora infestans, and the other 8 were mock-inoculated with sterile water. Leaf tissue samples from each replicate were taken at 12 hours before and 12, 36 and 60 hours after inoculation. We refer to 12 hours before inoculation as the h0 time point. Expression levels were obtained for 13440 genes.

Usage

data("phytophthora")

Format

A list with four matrices representing expression levels for 13440 genes (rows) in 16 replicates (columns) at time points "h0", "h12", "h36" and "h60". At each time point, the first 8 columns correspond to treatment (inoculated) replicates and the last 8 columns correspond to control (mock-inoculated) replicates. The names of the genes are the names of the rows in each matrix.

Details

For details about experimental conditions, see Restrepo et al. (2005) and Cai et al. (2013).

Source

Tomato Expression Database website (http://ted.bti.cornell.edu/), experiment E022 (Restrepo et al., 2005).

References

Restrepo, S., Cai, G., Fry, W. E. and Smart, C. D. (2005) Gene expression profiling of infection of tomato by Phytophthora infestans in the field. Phytopathology, 95(S88).

Cai, G., Restrepo, S., Myers, K., Zuluaga, P., Danies, G., Smart, C. and Fry W.E. (2013) Gene profiling in partially resistant and susceptible near-isogenic tomatoes in response to late blight in the field. Molecular plant pathology, 14(2): 171–184.

Examples

for(tp in 1:4){
    cat(paste("Time Point:", names(phytophthora[tp]), "\n"))
    print(phytophthora[[tp]][1:10,])
    cat("...\n \n")
}

acde documentation built on Nov. 8, 2020, 11:10 p.m.