WBPaper00035429:UVC_downregulated

For both analyses, authors made the following comparisons: control vs. UVC-exposed in each strain (three total); all pairwise strain comparisons under control conditions (three total); and all pair-wise strain comparisons after UVC exposure (three total). Genes downregulated by UVC exposure in all three strains (N2, glp-1, xpa-1).

WBPaper00035429:UVC_upregulated

For both analyses, authors made the following comparisons: control vs. UVC-exposed in each strain (three total); all pairwise strain comparisons under control conditions (three total); and all pair-wise strain comparisons after UVC exposure (three total). Genes upregulated by UVC exposure in all three strains (N2, glp-1, xpa-1).

WBPaper00040426:CYD-1_CDK-4_downregulated

Statistical analysis was through MAANOVA. In a fixed effect analysis, sample, array, and dye effects were modeled. P-values were determined by a permutation F2-test, in which residuals were shuffled 5000 times globally. Probes with p < 0.05 after family-wise error correction were considered significantly changed. Genes downregulated by CYD-1/CDK-4 for more than two fold.

WBPaper00040426:CYE-1_CDK-2AF_downregulated

Statistical analysis was through MAANOVA. In a fixed effect analysis, sample, array, and dye effects were modeled. P-values were determined by a permutation F2-test, in which residuals were shuffled 5000 times globally. Probes with p < 0.05 after family-wise error correction were considered significantly changed. Genes downregulated by CYE-1/CDK-2AF for more than two fold.

WBPaper00045015:acs-3(ft5)_downregulated

Pair-wise significance testing (mutant/RNAi vs. wild-type/vector) was performed using the Bioconductor package limma and p-values were initially corrected for multiple testing using the false discovery rate (FDR) method of Benjamini and Hochberg. Authors defined differential expression as log2(ratio) >= 0.848 with the FDR set to 5%, and p-value <= 0.001. Genes down-regulated in acs-3(ft5) mutants.

WBPaper00045015:acs-3(ft5)_upregulated

Pair-wise significance testing (mutant/RNAi vs. wild-type/vector) was performed using the Bioconductor package limma and p-values were initially corrected for multiple testing using the false discovery rate (FDR) method of Benjamini and Hochberg. Authors defined differential expression as log2(ratio) >= 0.848 with the FDR set to 5%, and p-value <= 0.001. Genes up-regulated in acs-3(ft5) mutants.

WBPaper00040426:CYD-1_CDK-4_upregulated

Statistical analysis was through MAANOVA. In a fixed effect analysis, sample, array, and dye effects were modeled. P-values were determined by a permutation F2-test, in which residuals were shuffled 5000 times globally. Probes with p < 0.05 after family-wise error correction were considered significantly changed. Genes upregulated by CYD-1/CDK-4 for more than two fold.

WBPaper00040426:CYE-1_CDK-2AF_upregulated

Statistical analysis was through MAANOVA. In a fixed effect analysis, sample, array, and dye effects were modeled. P-values were determined by a permutation F2-test, in which residuals were shuffled 5000 times globally. Probes with p < 0.05 after family-wise error correction were considered significantly changed. Genes upregulated by CYE-1/CDK-2AF for more than two fold.

WBPaper00045015:nhr-25(RNAi)_upregulated

Pair-wise significance testing (mutant/RNAi vs. wild-type/vector) was performed using the Bioconductor package limma and p-values were initially corrected for multiple testing using the false discovery rate (FDR) method of Benjamini and Hochberg. Authors defined differential expression as log2(ratio) >= 0.848 with the FDR set to 5%, and p-value <= 0.001. Genes up-regulated following nhr-25(RNAi).

WBPaper00040998:nhr-80_regulated

Pair-wise significance testing (mutant vs. wild-type) was performed using the Bioconductor package limma and p-values were initially corrected for multiple testing using the false discovery rate (FDR) method of Benjamini and Hochberg. Criteria for differential expression was set by employing log2(ratio) >= 0.848 and p-value < 0.001. Differentially expressed genes in nhr-80(tm1011) compared to wild-type animals using microarray analysis.