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.

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.

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.

WBPaper00027758:Group_II

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 lower expression in efl-1, dpl-1 and lin-35 mutants than in control gonads.

WBPaper00027758:Regulated_genes_not_in_group

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 whose expression is either up- or downregulated in efl-1, dpl-1 or lin-35 mutants relative to controls.

WBPaper00027758:Group_IV

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 significantly increased expression levels only in the lin-35 mutant relative to controls.

WBPaper00049325:CB4856_vs_N2_DEG

To identify proteins that are differentially expressed between N2 and CB4856, SILAC data were filtered for proteins that were quantified at least twice with at least a 1.3-fold difference in abundance and a p-value < 0.000457 (z-test, permutation determined threshold with the FDR cutoff of 0.05). Proteins that showed differential expression between CB4856 and N2 animals.