WBPaper00060526:plp-1(ok2155)_downregulated

DESeq2. Genes with at least 2-fold upregulation with a raw P value <= 0.05 only are listed. Transcripts that showed significantly decreased expression in plp-1(ok2155) adult animals comparing to in wild type.

WBPaper00060526:plp-1(ok2155)_upregulated

DESeq2. Genes with at least 2-fold upregulation with a raw P value <= 0.05 only are listed. Transcripts that showed significantly increased expression in plp-1(ok2155) adult animals comparing to in wild type.

WBPaper00042236:flcn-1(ok975)_upregulated

Agilent microarray raw data were processed and quantile normalized with the marray package from the Bioconductor project. Fold change statistics and Students t-test were used to create lists of candidates for differential gene expression. Transcripts that showed significantly increased expression in RB1035[flcn-1(ok975)] comparing to in N2 at young adult stage.

WBPaper00042527:age_dependent_miRNA

Details available in Supplementary material of the paper. Diff Exp, is the approximate ratio of expression comparing Young to Old animals (11 day difference in age). The raw p-value is for the null hypothesis that the Diff exp Ratio = 1 (based on robust inference - see supplemental information) and the associated 95% CI of the ratio. miRNAs with age dependent abundance in wild type animals.

WBPaper00037147:heatshock_downregulated

Survival during heat stress was analyzed using a non-parametric (Mantel-Haenszel) Log rank test and presented as Kaplan-Meier survival curves (Prism software package). For the TSA analysis all full genome wide expression analyses involved comparisons of two groups and thus on a gene by gene basis, for each set, authors performed two-sample t-tests on the log2 transformed expression measures to derive raw p-values. The Benjamini and Hochberg was then used to report the inference adjusted for multiple comparisons (q-values), in their case controlling false discovery rate (FDR). Statistically significant differential expression was defined as FDR q-value <= 0.05, thereby controlling FDR at <= 0.05 for each set of comparisons. Shown here are heat shock vs control ratio and raw p_value based on two-sample t-test. Genes for which heat shock F3 (fraction 3, containing heavy polysomes) versus control F3 is significantly decreased

WBPaper00040876:mir-35_downregulated

The raw data was normalized and t-statics were computed using R and Bioconductor with the affy package and Benjamini-Hoch-berg (BH) correction method for multiple comparisons. RNA levels that changed at least 1.5-fold with a probability of p < 0.005 after BH correction were considered significantly different in mir-35(gk262) mutants relative to wild-type. Genes with expression level down regulated in mir-35 mutants comparing with N2.

WBPaper00040876:mir-35_upregulated

The raw data was normalized and t-statics were computed using R and Bioconductor with the affy package and Benjamini-Hoch-berg (BH) correction method for multiple comparisons. RNA levels that changed at least 1.5-fold with a probability of p < 0.005 after BH correction were considered significantly different in mir-35(gk262) mutants relative to wild-type. Genes with expression level up regulated in mir-35 mutants comparing with N2.

WBPaper00037147:heatshock_upregulated

Survival during heat stress was analyzed using a non-parametric (Mantel-Haenszel) Log rank test and presented as Kaplan-Meier survival curves (Prism software package). For the TSA analysis all full genome wide expression analyses involved comparisons of two groups and thus on a gene by gene basis, for each set, authors performed two-sample t-tests on the log2 transformed expression measures to derive raw p-values. The Benjamini and Hochberg was then used to report the inference adjusted for multiple comparisons (q-values), in their case controlling false discovery rate (FDR). Statistically significant differential expression was defined as FDR q-value <= 0.05, thereby controlling FDR at <= 0.05 for each set of comparisons. Shown here are heat shock vs control ratio and raw p_value based on two-sample t-test. Genes for which heat shock F3 (fraction 3, containing heavy polysomes) versus control F3 is significantly increased.

WBPaper00046496:Rifampicin_upregulated

The primary data was analyzed with Affymetrix Expression Console. Further differential gene expression was performed using Genespring GX 11.1 with Affymetrix default analysis settings and RMA was used for normalization. The probes of intensities less than 20 percentile in the raw data were excluded prior to differential gene expression analysis. More than two fold expression changes with p value <0.05 (student's t test) are reported. Genes upregulated on Rifampicin treatment determined by Microarray analysis.

WBPaper00046496:Rifampicin_downregulated

The primary data was analyzed with Affymetrix Expression Console. Further differential gene expression was performed using Genespring GX 11.1 with Affymetrix default analysis settings and RMA was used for normalization. The probes of intensities less than 20 percentile in the raw data were excluded prior to differential gene expression analysis. More than two fold expression changes with p value <0.05 (student's t test) are reported. Genes downregulated on Rifampicin treatment determined by Microarray analysis.