- 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.
- 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.
- WBPaper00035654:alpha-synuclein_regulated
TIGR Spotfinder software was used to filter unreliable spots based on Otsu's method algorithm and to convert good spots in microarray images to numerical form. Raw signal values were analyzed using mean centering to normalize signal values between channels. Signals from Alexa Fluor Dye Control probes were excluded from normalization process due their oversaturation leaving only probe intensities from C. elegans miRNAs to use in normalization. Signal intensity ratios were calculated for each signal pair yielding fold change values and p values for each miRNAs from the strain of investigation. A cutoff of 1.4 was used to detect modestly changing miRNAs.
Genes that differentially expressed in WBPaper00035654Is1[aex-3
- WBPaper00035654:cat-1(e1111)_regulated
TIGR Spotfinder software was used to filter unreliable spots based on Otsu's method algorithm and to convert good spots in microarray images to numerical form. Raw signal values were analyzed using mean centering to normalize signal values between channels. Signals from Alexa Fluor Dye Control probes were excluded from normalization process due their oversaturation leaving only probe intensities from C. elegans miRNAs to use in normalization. Signal intensity ratios were calculated for each signal pair yielding fold change values and p values for each miRNAs from the strain of investigation. A cutoff of 1.4 was used to detect modestly changing miRNAs.
Genes that differentially expressed in cat-1(e1111) comparing with N2 at L4 larva.
- WBPaper00035654:pdr-1(gk448)_regulated
TIGR Spotfinder software was used to filter unreliable spots based on Otsu's method algorithm and to convert good spots in microarray images to numerical form. Raw signal values were analyzed using mean centering to normalize signal values between channels. Signals from Alexa Fluor Dye Control probes were excluded from normalization process due their oversaturation leaving only probe intensities from C. elegans miRNAs to use in normalization. Signal intensity ratios were calculated for each signal pair yielding fold change values and p values for each miRNAs from the strain of investigation. A cutoff of 1.4 was used to detect modestly changing miRNAs.
Genes that differentially expressed in pdr-1(gk448) comparing with N2 at L4 larva.
- WBPaper00035424:ASER_up
Intensities of spot features annotated as Bad or Not Found in the .gpr files were set to 1 to be removed from further analysis, and all of the six processed .gpr data were converted to .mev file with TIGR ExpressConverter ver. 1.7. The .mev files were processed with TIGR MIDAS ver. 2.19 with parameters set as follows: one bad channel tolerance policy as generous, with both of channel flag checked and background unchecked. The data were normalized by lowess normalization with default settings and with block and slide SD regularization. Authors then calculated log2(ASER/ASEL) ratios for each gene on the microarray. For the two pairs of dye-swapped repeats, authors calculated the mean log2(ASER/ASEL) of each repeat, so that up to four log2(ASER/ASEL) values per spot were obtained. Authors then calculated the percentile rank for each gene. Each gene spot detected more than once (18 847 spots) were subjected to MannWhitneys U test to assess whether its percentile rank values are significantly higher compared to the rest of the genes detected in the same experiments. Resulting significance levels are shown by P-values. From the P-values, false discovery rate (FDR) was further calculated by the Benjamini and Hochberg method. Statistical analyses were done by using R software version 2.9.
Genes that showed higher expression level in ASER than in ASEL neuron by mRNA tagging.
- WBPaper00035424:ASER_down
Intensities of spot features annotated as Bad or Not Found in the .gpr files were set to 1 to be removed from further analysis, and all of the six processed .gpr data were converted to .mev file with TIGR ExpressConverter ver. 1.7. The .mev files were processed with TIGR MIDAS ver. 2.19 with parameters set as follows: one bad channel tolerance policy as generous, with both of channel flag checked and background unchecked. The data were normalized by lowess normalization with default settings and with block and slide SD regularization. Authors then calculated log2(ASER/ASEL) ratios for each gene on the microarray. For the two pairs of dye-swapped repeats, authors calculated the mean log2(ASER/ASEL) of each repeat, so that up to four log2(ASER/ASEL) values per spot were obtained. Authors then calculated the percentile rank for each gene. Each gene spot detected more than once (18 847 spots) were subjected to MannWhitneys U test to assess whether its percentile rank values are significantly higher compared to the rest of the genes detected in the same experiments. Resulting significance levels are shown by P-values. From the P-values, false discovery rate (FDR) was further calculated by the Benjamini and Hochberg method. Statistical analyses were done by using R software version 2.9.
Genes that showed lower expression level in ASER than in ASEL neuron by mRNA tagging.