[cgc5767]:expression_class_MDE

A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. Maternal degradation-embryonic class (MDE): genes that are the subset of maternal degradation genes that significantly increase in at least two of the eight total paired timepoint tests in the induction-following-degradation time domain.

WBPaper00030839:Larval_A_Class

A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets. Larval A-class motor neuron enriched genes.

WBPaper00030839:Embryo_A_Class

A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets. Embryonic A-class motor neuron enriched genes.

WBPaper00032454:IR_upregulated

To identify differentially expressed genes, gene expression intensity was compared using a moderated t-test and a Bayes smoothing approach developed for a low number of replicates. Genes up-regulated following ionizing radiation (IR) treatment.

WBPaper00026640:Development_Group_III

N.A. The expression of group III proteins exhibited a sharp decline and remained at a relatively low level in postembryonic development.

WBPaper00055226:ADR-2_target_N2

DESeq2, p-value < 0.05 and a fold enrichment log2fold > 0.5. Genes that exhibit a differential enrichment (p-value < 0.05 and a fold enrichment (log2fold)> 0.5) between the ADR-2 IPs from N2 and adr-2(ok735)worms.

WBPaper00065746:eat-2(ad1113)_upregulated

DESeq2. The genes with a fold change >= 2 and a false discovery rate (FDR) < 0.05 in a comparison were identified as significant DEGs. Transcripts that showed significantly increased expression in eat-2(ad1113) comparing to in N2.

WBPaper00065746:tmc-1(rg1003)_upregulated

DESeq2. The genes with a fold change >= 2 and a false discovery rate (FDR) < 0.05 in a comparison were identified as significant DEGs. Transcripts that showed significantly increased expression in tmc-1(rg1003) comparing to in N2.

WBPaper00036464:S.aureus-RN6390_regulated

The two conditions were then compared in Resolver to determine fold change for each probe set and a p-value, using a modified t test. Genes with a 2-fold or greater fold change and a p-value ,0.01 were considered differentially expressed. Genes with altered expression after 8 h S. aureus infection.

WBPaper00065746:tmc-1(rg1003)_downregulated

DESeq2. The genes with a fold change >= 2 and a false discovery rate (FDR) < 0.05 in a comparison were identified as significant DEGs. Transcripts that showed significantly decreased expression in tmc-1(rg1003) comparing to in N2.