5 Expression clusters found (0.006 seconds)

- WBPaper00050332:juglone_upregulated
- WBPaper00046853:AOBr_M.aeruginosa-batch-culture_upregulated
- WBPaper00046853:AOBr_M.aeruginosa-batch-culture_downregulated
- WBPaper00033444:bacteria_regulated
- [cgc5767]:expression_class_M

Using the Cufflink package and CuffDiff application from Galaxy, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were calculated and tested for differential expression with a FDR score of 5%.
Transcripts that showed significantly increased expression after exposed to 38 M juglone for 3 hours.

Differentially expressed genes (DEGs) were identified with a random variance t-test and a significance analysis of microarrays (SAM) test. Genes were considered statistically significant if their p-value was less than 0.05, the false discovery rate less than 0.3, and the fold change compared to control at least <= 0.67 or >=1.5.
Genes that showed significantly increased expression after exposure to adsorbable organic bromine compounds (AOBr) contained in M. aeruginosa batch culture.

Differentially expressed genes (DEGs) were identified with a random variance t-test and a significance analysis of microarrays (SAM) test. Genes were considered statistically significant if their p-value was less than 0.05, the false discovery rate less than 0.3, and the fold change compared to control at least <= 0.67 or >=1.5.
Genes that showed significantly decreased expression after exposure to adsorbable organic bromine compounds (AOBr) contained in M. aeruginosa batch culture.

Data was analyzed using SAS statistical software (SAS Institute Inc., Cary, North Carolina, USA) using a two-step mixed model analysis of variance to account for all possible sources of variance. This two-step ANOVA was performed using the MIXED procedure in SAS.
Significantly differentially expressed genes after different bacteria treatment. Transcriptional responses of wild-type C. elegans adults were assayed after growth on each of the four bacteria - E. coli, M. luteus, Pseudomonas sp., or B. megaterium. These genes were differentially expressed and statistically significant with multiple testing correction (q < 0.01) across all pair-wise comparisons.

A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing.
Maternal class (M): genes that are called present in at least one of the three PC6 replicates.