- WBPaper00041174:environmental_prime
two-way ANOVA
Genes with significant variation in expression level only across environments(control, 25C, High-pH-Salt, Liquid, infection), but no genotypic variation (AB2, CB4856, RC301, CB4857, N2, HC445).
- WBPaper00041174:genotypic
two-way ANOVA
Genes with variation in expression level across genotypes (AB2, CB4856, RC301, CB4857, N2, HC445).
- WBPaper00041174:environmental
two-way ANOVA
Genes with variation in expression level across conditions (control, 25C, High-pH-Salt, Liquid, infection).
- WBPaper00041174:genotype_environment_interaction
two-way ANOVA
Genes with significant variation in expression level with genotype-environment interaction. Expression of these genes change when there are certian combinations of genotype-environment. Genotypes
- WBPaper00041174:genotypic_prime
two-way ANOVA
Genes with significant variation in expression level only across genotypes(AB2, CB4856, RC301, CB4857, N2, HC445), but not environments (control, 25C, High-pH-Salt, Liquid, infection).
- WBPaper00039866:ClassComp_daf-19_downregulated
BRB Array Tools (version 3.3) was subsequently used to identify genes with a statistically significant variation in expression when comparing between the two classes defined in this study. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically different. Genes with a signal variation of 1.5-fold or greater were selectively identified for use in all subsequent experiments. To reduce the chances of false discoveries, a class comparison test was conducted using a multivariate permutation test with the confidence level of 97%.
Candidate daf-19 down regulated genes with a statistically significant signal variation of 1.5-fold or greater. These were identified using a class comparisons tool from BRB Array Tools.
- WBPaper00039866:SAM_daf-19_upregulated
Lists of genes were generated using SAM (version 2.2) with a false discovery rate (FDR) of less than or equal to 5% (Q-value <= 5%). Twenty-seven repeated runs of SAM were performed using variable random seed numbers for each run. During each run of SAM, 100 permutations were performed. Genes (n =129 downregulated, n = 1 upregulated) appearing in at least 80% of all twenty-seven runs of SAM were further considered for signal variation filtering, which was used to selectively identify genes with a 1.5-fold or greater variation between the two genetic conditions used for comparison.
Candidate daf-19 up regulated genes with a statistically significant signal variation of 1.5-fold or greater. These were identified using a Significance Analysis of Microarrays (SAM).
- WBPaper00039866:SAM_daf-19_downregulated
Lists of genes were generated using SAM (version 2.2) with a false discovery rate (FDR) of less than or equal to 5% (Q-value <= 5%). Twenty-seven repeated runs of SAM were performed using variable random seed numbers for each run. During each run of SAM, 100 permutations were performed. Genes (n =129 downregulated, n = 1 upregulated) appearing in at least 80% of all twenty-seven runs of SAM were further considered for signal variation filtering, which was used to selectively identify genes with a 1.5-fold or greater variation between the two genetic conditions used for comparison.
Candidate daf-19 down regulated genes with a statistically significant signal variation of 1.5-fold or greater. These were identified using a Significance Analysis of Microarrays (SAM).
- WBPaper00039866:ClassComp_daf-19_upregulated
BRB Array Tools (version 3.3) was subsequently used to identify genes with a statistically significant variation in expression when comparing between the two classes defined in this study. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically different. Genes with a signal variation of 1.5-fold or greater were selectively identified for use in all subsequent experiments. To reduce the chances of false discoveries, a class comparison test was conducted using a multivariate permutation test with the confidence level of 97%.
Candidate daf-19 up regulated genes with a statistically significant signal variation of 1.5-fold or greater. These were identified using a class comparisons tool from BRB Array Tools.