- WBPaper00031903:prg-1_regulated
The fold differences from the three experiments were averaged, and a Z test [Z = (observed - expected) / SE] was performed. Genes with up- or downregulation greater than 1.5-fold, p < 0.05, in any given mutant were selected for inclusion.
Genes with differential expression in prg-1(tm872) male gonads comparing to N2.
- 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.
- WBPaper00041207:CE_dauer_up
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 up regulated in the dauer versus dauer-exit worms.
- WBPaper00046156:eat-2(ad1116)_Day8_downregulated
A fold change >= 1.5 with a minimum read count of >= 10 were used to filter the differentially expressed miRNA. The p-value cutoff was set at p <= 0.05 based on Kals Z test statistical.
miRNAs that showed decreased expression in 8 days post L4 adult hermaphrodite eat-2(ad1116) comparing to in N2.
- WBPaper00046156:eat-2(ad1116)_Day1_upregulated
A fold change >= 1.5 with a minimum read count of >= 10 were used to filter the differentially expressed miRNA. The p-value cutoff was set at p <= 0.05 based on Kals Z test statistical.
miRNAs that showed increased expression in 1 day post L4 adult hermaphrodite eat-2(ad1116) comparing to in N2.
- WBPaper00046156:eat-2(ad1116)_Day8_upregulated
A fold change >= 1.5 with a minimum read count of >= 10 were used to filter the differentially expressed miRNA. The p-value cutoff was set at p <= 0.05 based on Kals Z test statistical.
miRNAs that showed increased expression in 8 days post L4 adult hermaphrodite eat-2(ad1116) comparing to in N2.
- WBPaper00027758:Group_I
For each set of mutant data, the repeats were averaged, and a Z test [Z=(observedexpected)\/SE] was performed in Excel. A moderate correction for multiple testing (~17,600 genes) was performed by multiplying the calculated P-value by 10,000. After this correction, all genes with up- or downregulation greater than twofold, P<0.05 in any given mutant were selected. The hypergeometric probability test was used to calculate the significance of overlap of gene groups. Authors determined whether transcripts of Group I-IV genes are bound by GLD-1, based on a minimum criteria of >1.5 enrichment in GLD-1 immunoprecipitated samples compared to control immunoprecipitations (P < 0.01).
Genes downregulated in dpl-1(n3316) and efl-1(n3639) mutants.
- WBPaper00038304:octr-1_regulated
Microarray data were subjected to the robust multichip averaging algorithm using GeneSpring GX software (Agilent Technologies, Santa Clara, CA). Analysis of variance t test and fold-change calculations were also performed using GeneSpring GX software. Probability calculations of enrichment were performed using the hypergeometric probability test (http://elegans.uky.edu/MA/progs/overlap_stats.html) to calculate the statistical significance of the overlap of gene groups.
Genes regulated by octr-1(ok371) after infected with P. aeruginosa PA14 for 4 hours at 25 centigrade.
- WBPaper00027758:Group_III
For each set of mutant data, the repeats were averaged, and a Z test [Z=(observedexpected)\/SE] was performed in Excel. A moderate correction for multiple testing (~17,600 genes) was performed by multiplying the calculated P-value by 10,000. After this correction, all genes with up- or downregulation greater than twofold, P<0.05 in any given mutant were selected. The hypergeometric probability test was used to calculate the significance of overlap of gene groups. Authors determined whether transcripts of Group I-IV genes are bound by GLD-1, based on a minimum criteria of >1.5 enrichment in GLD-1 immunoprecipitated samples compared to control immunoprecipitations (P < 0.01).
Genes with higher expression in one or more mutants of efl-1, dpl-1 and lin-35 relative to controls.