WBPaper00041606:PP_S.marcescens_regulated

Differential expression were calculated by empirical eBayes method using eBayes function. P_value <= 0.01 and log2 fold change > 1 were used to call differentially expressed genes in all datasets. Pristionchus pacificus Genes with expression levels changed significantly after treatment of Serratia marcescens.

WBPaper00041606:PP_X.nematophila_regulated

Differential expression were calculated by empirical eBayes method using eBayes function. P_value <= 0.01 and log2 fold change > 1 were used to call differentially expressed genes in all datasets. Pristionchus pacificus Genes with expression levels changed significantly after treatment of Xenorhabdus nematophila.

WBPaper00041606:PP_S.aureus_regulated

Differential expression were calculated by empirical eBayes method using eBayes function. P_value <= 0.01 and log2 fold change > 1 were used to call differentially expressed genes in all datasets. Pristionchus pacificus Genes with expression levels changed significantly after treatment of Staphylococcus aureus.

WBPaper00041606:PP_B.thuringiensis-DB27_regulated

Differential expression were calculated by empirical eBayes method using eBayes function. P_value <= 0.01 and log2 fold change > 1 were used to call differentially expressed genes in all datasets. Pristionchus pacificus Genes with expression levels changed significantly after treatment of Bacillus thurigiensis DB27.

WBPaper00041207:PP_dauer_down

The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function. Control of FDR was employed as correction for multiple testing. Pristionchus pacificus genes down regulated in the dauer versus dauer-exit worms.

WBPaper00041207:PP_dauer_up

The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function. Control of FDR was employed as correction for multiple testing. Pristionchus pacificus genes up regulated in the dauer versus dauer-exit worms.