- expression cluster: 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.
- expression cluster: 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.
- expression cluster: 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.
- expression cluster: 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.
- expression cluster: WBPaper00045473:PP_Germline_Conserved_Operon
Differential expression was calculated by empirical Bayes method using the eBayes function, and control of FDR was employed as the multiple testing correction. Authors used cutoff of absolute log2 fold change greater than or equal to 1.5 AND p_value less than or equal to 0.05 to call differentially expressed genes.
Germline expressed genes in P.pacificus are also significantly enriched in the annotated\/validated operons conserved across P.pacificus and C.elegans.
- expression cluster: 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.
- expression cluster: 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.
- expression cluster: WBPaper00041466:PP_germline-ablation_regulated
Differential expression was calculated by empirical Bayes method using the eBayes function, and control of FDR was employed as the multiple testing correction. Authors used cutoff of absolute log2 fold change greater than or equal to 1.5 AND p_value less than or equal to 0.05 to call differentially expressed genes.
Genes that showed differential expression in the comparision of germline-ablated animals fed on E. coli OP50 versus un-ablated animals fed E. coli OP50.
- expression cluster: WBPaper00041466:PP_S.marcescens_regulated
Differential expression was calculated by empirical Bayes method using the eBayes function, and control of FDR was employed as the multiple testing correction. Authors used cutoff of absolute log2 fold change greater than or equal to 1.5 AND p_value less than or equal to 0.05 to call differentially expressed genes.
Genes that showed differential expression in the comparison of germline-ablated animals fed on S. marcescens versus germline-ablated animals fed E. coli OP50.