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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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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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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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