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Pristionchus pacificus genes up regulated in the dauer versus dauer-exit worms. |
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. |
WBPaper00041207:PP_dauer_up
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Germline ablation |
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. |
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. |
WBPaper00041466:PP_germline-ablation_regulated
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Bacteria infection: Serratia marcescens |
Pristionchus pacificus Genes with expression levels changed significantly after treatment of Serratia marcescens. |
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. |
WBPaper00041606:PP_S.marcescens_regulated
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Transcripts that showed significantly increased expression in Ppa-sul-2(tu1069) animals comparing to in wild type PS312 animals at J4.12 stage. |
DESeq244(version 1.18.1) with two criteria, P-value < 0.05 and Fold change > 2. |
WBPaper00064862:Ppa-sul-2(tu1069)_J4.12_Up
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Germline ablation |
Genes that showed differential expression in the comparison of germline-ablated animals fed on S. marcescens versus germline-ablated animals fed E. coli OP50. |
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. |
WBPaper00041466:PP_S.marcescens_regulated
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Transcripts that showed significantly increased expression in Ppa-sul-2(tu1069) animals comparing to in wild type PS312 animals at 4M1 stage. |
DESeq244(version 1.18.1) with two criteria, P-value < 0.05 and Fold change > 2. |
WBPaper00064862:Ppa-sul-2(tu1069)_4M3_Up
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