- expression cluster: WBPaper00042258:DA1877_downregulated_YoungAdult
Moderated T statistics in Limma was used to calculate significance. Significance was determined using an adjusted p value. Changes in gene expression that were 2-fold (p < 0.001) or greater were considered significantly changed.
Genes downregulated on Comamonas DA1877 relative to E. coli OP50, Young adult
- expression cluster: WBPaper00044005:DAF-16_upregulated
Authors reanalyzed raw genome-wide expression data from five studies (McElwee et al., 2003; McElwee et al., 2004; Murphy et al., 2003; Shaw et al., 2007; Troemeletal.,2006) encompassing 75 genome-wide expression profiles, which authors used to construct 46 explicit contrasts between conditions with differing levels of DAF-16 activity. After complete reprocessing of the raw data (array-specific standardization, normalization, and remapping of probes), a log-fold-change and corresponding standard error were calculated for each transcript on each array (or array pair for single-channel technologies). Together, these were converted into a vote value between 1 (highly likely to be downregulated) and +1 (highly likely to be upregulated). The total voting score for each gene was computed as the sum of voting scores for individual experiments, which is robust in the sense that the influence of any individual experiment is limited to a single full vote. An empirical null distribution based on random permutation was created, and all genes were ranked from consistently upregulated (class I) to consistently downregulated (class II). The area under the null distribution (p value) for each gene that served as the basis for assigning genes to class I or class II at a 5% false discovery rate.
Top 50 up regulated genes by DAF-16 based on reanalysis 75 previously published experiments.
- expression cluster: WBPaper00044030:nhr-8(hd117)_downregulated
Expression data were read in the statistical programming environment R and processed for background correction and quantile normalization and summarized for genes that differed in expression >= 1.5-fold (N2 versus nhr-8) and a p value <= 0.01 using the Limma package.
Genes that showed decreased expression in nhr-8(hd117) comparing to N2.
- expression cluster: WBPaper00044091:Bpseudomallei_induced_2h
After array normalization, significance analysis of microarray was performed on data from individual time points (two class unpaired response) to identify genes with small but consistent changes. A false-discovery rate (FDR) of ~1% was used as criteria to consider a gene differentially regulated.Authors chose this particular FDR because it was the lowest FDR that did not significantly reduce the number of estimated true positives.
Genes that showed increased expression in adult animals after 2 hour exposure to B. pseudomallei R15 vs. exposure to OP50.
- expression cluster: WBPaper00044091:Bpseudomallei_induced_4h
After array normalization, significance analysis of microarray was performed on data from individual time points (two class unpaired response) to identify genes with small but consistent changes. A false-discovery rate (FDR) of ~1% was used as criteria to consider a gene differentially regulated.Authors chose this particular FDR because it was the lowest FDR that did not significantly reduce the number of estimated true positives.
Genes that showed increased expression in adult animals after 4 hour exposure to B. pseudomallei R15 vs. exposure to OP50
- expression cluster: WBPaper00044316:CH3HgCl_7.5uM_downregulated
Rosetta Resolver was used to identify differentially expressed genes using an error-weighted, 1-way ANOVA with a Bonferroni correction. A 2-fold change in expression, relative to untreated controls, and a p-value < 0.01 was required for a gene to qualify as significantly, differentially expressed.
Genes that showed decreased expression after exposure to 7.5uM CH3HgCl for 24 hours.
- expression cluster: WBPaper00044535:male_downregulated
To identify significantly regulated genes between the -male and +male conditions, authors used the Rank Products methods (R package RankProd), using the batch information to adujst for experiment specific biases, and set a False Discovery Rate (FDR) threshold for discovery of genes of 5%. From this analysis, 341 probes on the array were significantly up-regulated in the male treated samples, and 289 were significantly down-regulated.
Genes down regulated in hermaphrodites after 8 days of exposure to males.