WBPaper00048926:miaserin_upregulated_adult-day3

The quasi-likelihood F-test from the edgeR package was used to test these counts for statistically significant differential gene expression between water- and mianserin-treated samples, while controlling for expression differences between the 3 biological replicates. We performed multiple testing correction by using the Benjamini-Hochberg procedure to compute a false discovery rate (FDR) value for each gene, and we considered an FDR less than 10% to be significant. Genes that increased expression in response to 50uM mianserin on adult day 3, which are not a response to aging. This is a list of 111 genes.

WBPaper00048926:miaserin_upregulated_adult-day5

The quasi-likelihood F-test from the edgeR package was used to test these counts for statistically significant differential gene expression between water- and mianserin-treated samples, while controlling for expression differences between the 3 biological replicates. We performed multiple testing correction by using the Benjamini-Hochberg procedure to compute a false discovery rate (FDR) value for each gene, and we considered an FDR less than 10% to be significant. Genes that increased expression in response to 50uM mianserin on adult day 5, which are not a response to aging. This is a list of 733 genes.

WBPaper00048926:miaserin_upregulated_adult-day10

The quasi-likelihood F-test from the edgeR package was used to test these counts for statistically significant differential gene expression between water- and mianserin-treated samples, while controlling for expression differences between the 3 biological replicates. We performed multiple testing correction by using the Benjamini-Hochberg procedure to compute a false discovery rate (FDR) value for each gene, and we considered an FDR less than 10% to be significant. Genes that increased expression in response to 50uM mianserin on adult day 10, which are not a response to aging. This is a list of 138 genes.

WBPaper00026980:intestine_enriched

To identify genes that are significantly enriched by mRNA tagging, we first normalized the total amount of Cy3 and Cy5 signal to each other in each hybridization. We measured the ratio of the signals from the co-immunoprecipitated mRNA (Cy5) to total RNA in the cell extract (Cy3), and calculated the percentile rank for each gene relative to all genes in each hybridization. The mean percentile rank was determined from eight repeats of the mRNA-tagging experiment. Student's t-test was used to determine which genes showed a mean enrichment significantly greater than the median enrichment for all genes (P<0.001). Genes enriched in intestine.

WBPaper00046548:dafachronic-acid_upregulated

To identify the differentially expressed genes, we applied Significance Analysis of Microarrays (SAM) analysis using the R package samr [46]. Genes with median false discovery <5% and fold changes >2.0 were considered differentially expressed. Genes that showed significantly increased experssion after 22.5 hours of treatment in 200nM delta7-dafachronic acid comparing with in ethanol vehicle control.

WBPaper00046548:dafachronic-acid_downregulated

To identify the differentially expressed genes, we applied Significance Analysis of Microarrays (SAM) analysis using the R package samr [46]. Genes with median false discovery <5% and fold changes >2.0 were considered differentially expressed. Genes that showed significantly decreased experssion after 22.5 hours of treatment in 200nM delta7-dafachronic acid comparing with in ethanol vehicle control.

WBPaper00046415:lithium_downregulated

All data were analyzed using Stat View J 5.0, with all experimental data checked for assumptions of homogeneity of variance across manipulations using Bartletts test. Once the assumptions were satisfied, the data were analyzed by one-way analysis of variance followed by Dunnetts multiple comparison test. When homogeneity was not evident in the data, we used the nonparametric KruskalWallis test, followed by the MannWhitney U-test with a Bonferroni adjustment. Differences were considered significant at P < 0.05. Genes suppressed following 24h exposure to lithium compounds (78uM LiCl and 375uM Li2CO3), according to custom DNA microarray.

WBPaper00032430:rheb-1_regulated

Statistical analysis was performed by one-way analysis of variance (ANOVA) with a Benjamini and Hochberg false discovery rate (BH-FDR 5 0.1) multiple testing correction followed by Tukey post-hoc tests using log-transformed data (GeneSpring). Three-thousand-and-thirty-one probe sets were identified to be regulated by fasting in control RNAi-treated worms. We defined RHEB-1-dependent or TOR-dependent genes as those in which the expression level induced by fasting was reduced to less than half under rheb-1 RNAi or TOR (let-363) RNAi conditions. Fasting-induced upregulated genes whose induction is suppressed by rheb-1 RNAi.

WBPaper00031252:AIN-1_IP_enriched

Signals from replicates of total worm lysates from wt and strains containing the ain-2::gfp or the ain-2 promoter::gfp transgene were mean normalized and averaged respectively to generate standard profiles of gene expression in these worm strains. Authors then calculated the ratio of signal of each gene from each IP sample to the standard gene expression profile of the corresponding worm strain. Based on this ratio, a percentile rank of each gene relative to all genes in each IP replicate was calculated. The percentile ranks in the three replicates of each IP were averaged. Student t test was utilized to determine if the average percentile ranks of enrichment of individual genes were significantly higher (p value) than the mean enrichment of all genes in the IP samples. To determine the AIN-1 or AIN-2 associated genes, we used the following criteria: (1) average percentile ranks of enrichment is greater than the mean enrichment of all genes in AIN-1 or AIN-2 IP with p < 0.01; (2) average signal in AIN-1 or AIN-2 IP replicates is greater than the background signal (including 2X standard deviation (SD)) (Background signal and SD were calculated based on signals from empty spots on each microarray); (3) criteria 1 is not be satisfied for the same gene in the corresponding control IP. mRNAs that were significantly enriched in the AIN-1 immunoprecipitation samples, compared to the control total mRNAs in the input extracts (p < 0.01).

WBPaper00031252:AIN-2_IP_enriched

Signals from replicates of total worm lysates from wt and strains containing the ain-2::gfp or the ain-2 promoter::gfp transgene were mean normalized and averaged respectively to generate standard profiles of gene expression in these worm strains. Authors then calculated the ratio of signal of each gene from each IP sample to the standard gene expression profile of the corresponding worm strain. Based on this ratio, a percentile rank of each gene relative to all genes in each IP replicate was calculated. The percentile ranks in the three replicates of each IP were averaged. Student t test was utilized to determine if the average percentile ranks of enrichment of individual genes were significantly higher (p value) than the mean enrichment of all genes in the IP samples. To determine the AIN-1 or AIN-2 associated genes, we used the following criteria: (1) average percentile ranks of enrichment is greater than the mean enrichment of all genes in AIN-1 or AIN-2 IP with p < 0.01; (2) average signal in AIN-1 or AIN-2 IP replicates is greater than the background signal (including 2X standard deviation (SD)) (Background signal and SD were calculated based on signals from empty spots on each microarray); (3) criteria 1 is not be satisfied for the same gene in the corresponding control IP. mRNAs that were significantly enriched in the AIN-2 immunoprecipitation samples, compared to the control total mRNAs in the input extracts (p < 0.01).