WBPaper00053140:SustainedResponse_20nmAgCit

Differentially expressed genes were selected using one-way analysis of variance (ANOVA) based on Welch t-test. To improve moderated t-statistics, the I/NI-calls gene filtering procedure was applied before the Welch t-test to exclude non-informative genes. For each comparison between two experimental groups, the fold change (FC) of every annotated gene, together with their corresponding p-value, was used for selection of differentially expressed genes with cutoffs of p < 0.05 and FC > 1.5. Transcripts that showed sustained response after C. elegans adults were exposed to 100 ug per mL 20nmAgCit in CeHM for 4, 8 or 24 h.

WBPaper00053140:DecreasingResponse_20nmAgCit

Differentially expressed genes were selected using one-way analysis of variance (ANOVA) based on Welch t-test. To improve moderated t-statistics, the I/NI-calls gene filtering procedure was applied before the Welch t-test to exclude non-informative genes. For each comparison between two experimental groups, the fold change (FC) of every annotated gene, together with their corresponding p-value, was used for selection of differentially expressed genes with cutoffs of p < 0.05 and FC > 1.5. Transcripts that showed early or decreasing response after C. elegans adults were exposed to 100 ug per mL 20nmAgCit in CeHM for 4, 8 or 24 h.

WBPaper00049336:aptf-1(gk794)_downregulated_3-fold-embryo

Statistical tests used were Wilcoxon Signed Paired Ranks test, Students t-test or Welch test using Origin software. Error bars are SEM. Genes with significantly decreased expression in aptf-1(gk794) mutant in pretzel-stage comparing to in N2.

WBPaper00049336:aptf-1(gk794)_downregulated_L4

Statistical tests used were Wilcoxon Signed Paired Ranks test, Students t-test or Welch test using Origin software. Error bars are SEM. Genes with significantly decreased expression in aptf-1(gk794) mutant in L4 larva sleep stage comparing to in N2.

WBPaper00049336:aptf-1(gk794)_upregulated_L4

Statistical tests used were Wilcoxon Signed Paired Ranks test, Students t-test or Welch test using Origin software. Error bars are SEM. Genes with significantly increased expression in aptf-1(gk794) mutant in L4 larva sleep stage comparing to in N2.

WBPaper00053140:IncreasingResponse_20nmAgCit

Differentially expressed genes were selected using one-way analysis of variance (ANOVA) based on Welch t-test. To improve moderated t-statistics, the I/NI-calls gene filtering procedure was applied before the Welch t-test to exclude non-informative genes. For each comparison between two experimental groups, the fold change (FC) of every annotated gene, together with their corresponding p-value, was used for selection of differentially expressed genes with cutoffs of p < 0.05 and FC > 1.5. Transcripts that showed late or increasing response after C. elegans adults were exposed to 100 ug per mL 20nmAgCit in CeHM for 4, 8 or 24 h.

WBPaper00049336:aptf-1(gk794)_upregulated_3-fold-embryo

Statistical tests used were Wilcoxon Signed Paired Ranks test, Students t-test or Welch test using Origin software. Error bars are SEM. Genes with significantly increased expression in aptf-1(gk794) mutant in pretzel-stage comparing to in N2.

WBPaper00045374:Benzene_upregulated

Fold change and Welch t-test were applied to select differentially expressed genes (DEGs): the fold change threshold was 2-fold and the significance level, p < 0.05. Genes that showed increased expression after 24 hour exposure to 1 mg/L of benzene.

WBPaper00045374:Benzene_downregulated

Fold change and Welch t-test were applied to select differentially expressed genes (DEGs): the fold change threshold was 2-fold and the significance level, p < 0.05. Genes that showed decreased expression after 24 hour exposure to 1 mg/L of benzene.

WBPaper00049290:rsks-1(sv31)_upregulated

Two statistical approached were used to calculate P values: (1) a moderated t-test implemented in the LIMMA BioConductor package (primary P value), and the Welch statistical test (secondary P value). The statistical significance criteria were defined as 1.8-fold difference in expression levels with P values less than or equal to 0.05. Proteins that were significantly more abundant in Day-1 adult rsks-1(sv31) mutants compared to age-matched wild-type animals.