WBPaper00025099:MA_specific

Differentially-expressed genes in the MA lines.

WBPaper00034636:heat_shock_downregulated

paired t-tests Genes Showing Significant Expression Changes (P <= 0.05 After FDR) in Heat-Shocked (30 centigrade for 1.5 h; Two Arrays), Compared to Sham Controls (26 centigrade for 2.5 h; Five Arrays).

WBPaper00034636:heat_shock_upregulated

paired t-tests Genes Showing Significant Expression Changes (P <= 0.05 After FDR) in Heat-Shocked (30 centigrade for 1.5 h; Two Arrays), Compared to Sham Controls (26 centigrade for 2.5 h; Five Arrays).

WBPaper00006465:IV_ethanol_late_repression

Class IV genes are down-regulated at 6 h, but not at earlier time points.

WBPaper00065225:nhr-42(tm1375)_upregulated_S.aureus-infected

Adjusted p-value (Padj) <= 0.01 was considered significant for differential gene expression. Transcripts that showed significantly increased expression in nhr-42(tm1375) animals infected with S. aureus SH1000 for 5 h, comparing to in N2 animals infected with S. aureus SH1000 for 5 h.

WBPaper00065225:nhr-42(tm1375)_downregulated_S.aureus-infected

Adjusted p-value (Padj) <= 0.01 was considered significant for differential gene expression. Transcripts that showed significantly decreased expression in nhr-42(tm1375) animals infected with S. aureus SH1000 for 5 h, comparing to in N2 animals infected with S. aureus SH1000 for 5 h.

WBPaper00006465:II_ethanol_late_induction

Class II genes are those showing increase in transcript abundance at 6 h, but not at early time points.

WBPaper00047021:MWCNT_downregulated

N.A. Genes that showed significantly decreased expression after exposed to multiwall carbon nanotubes (MWCNTs) for 4 and 24 h.

WBPaper00047021:MWCNT_upregulated

N.A. Genes that showed significantly increased expression after exposed to multiwall carbon nanotubes (MWCNTs) for 4 and 24 h.

WBPaper00041207:CE_dauer_down

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. Genes dowm regulated in the dauer versus dauer-exit worms.