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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: Xenorhabdus nematophila |
Pristionchus pacificus Genes with expression levels changed significantly after treatment of Xenorhabdus nematophila. |
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_X.nematophila_regulated
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Protein that contains phosphorylation site according to nano-HPLC and mass spectrometry on enriched phosphopeptides. |
The database search results were parsed by MaxQuant to assemble protein groups, peptides, and phosphorylation sites at a false discovery rate of 1%. All phosphorylation events having a reported localization probability of at least 0.75 were considered as localized (assigned to a specific amino acid). |
WBPaper00041472:Phosphorylated_protein
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P.pacificus genes enriched in intestine. |
Cuffdiff (version v2.0.1) |
WBPaper00049334:PE_intestine_enriched
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Yeast culture: C.curvatus |
Transcripts that showed significantly decreased expression after fed with yeast culture C.curvatus, comparing to fed with OP50. |
Cuffdiff (version 2.0.1) |
WBPaper00050265:C.curvatus_vs_OP50_downregulated
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