- WBPaper00044260:nicotinc-acid_upregulated
Raw counts for the genes were analyzed using the R Statistical Computing Environment and the Bioconductor packages DESeq and edgeR. Both packages provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate (FDR). If both FDR values (by DESeq and edgeR) were smaller than p = 0.05, genes were assigned as differentially expressed.
Genes that showed increased expression after nicotic acid (NA) treatment.
- WBPaper00044260:nicotic-acid_downregulated
Raw counts for the genes were analyzed using the R Statistical Computing Environment and the Bioconductor packages DESeq and edgeR. Both packages provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate (FDR). If both FDR values (by DESeq and edgeR) were smaller than p = 0.05, genes were assigned as differentially expressed.
Genes that showed decreased expression after nicotic acid (NA) treatment.
- WBPaper00028789:PA14_vs_OP50_upregulated_4hr
At least 2 fold and P < 0.01, as determined by a t-test.
Genes upregulated in worms grown on P. aeruginosa PA14 as compared to worms grown on OP50 for 4 hours by at least 2 fold and P < 0.01, as determined by a t-test.
- WBPaper00028789:PA14_vs_OP50_downregulated_4hr
At least 2 fold and P < 0.01, as determined by a t-test.
Genes downregulated in worms grown on P. aeruginosa PA14 as compared to worms grown on OP50 for 4 hours by at least 2 fold and P < 0.01, as determined by a t-test.
- WBPaper00028789:PA14_vs_OP50_downregulated_8hr
At least 2 fold and P < 0.01, as determined by a t-test.
Genes downregulated in worms grown on P. aeruginosa PA14 as compared to worms grown on OP50 for 8 hours by at least 2 fold and P < 0.01, as determined by a t-test.
- WBPaper00028789:PA14_vs_OP50_upregulated_8hr
At least 2 fold and P < 0.01, as determined by a t-test.
Genes upregulated in worms grown on P. aeruginosa PA14 as compared to worms grown on OP50 for 8 hours by at least 2 fold and P < 0.01, as determined by a t-test.
- WBPaper00037849:sam-10(js94)_upregulated
Geometric mean=1.5 is used as a cutoff.
Genes with increased expression in sam-10(js94) mutants, revealed by microarray analysis. Geometric mean=1.5 is used as a cutoff.
- WBPaper00028789:pmk-1_downregulated
At least 2 fold and P < 0.01, as determined by a t-test.
Genes downregulated by wild-type pmk-1 (upregulated in daf-2(e1368);pmk-1(km25) strain as compared to daf-2(e1368) strain) by at least 2 fold and P < 0.01, as determined by a t-test.
- WBPaper00028789:pmk-1_upregulated
At least 2 fold and P < 0.01, as determined by a t-test.
Genes upregulated by wild-type pmk-1 (downregulated in daf-2(e1368);pmk-1(km25) strain as compared to daf-2(e1368) strain) by at least 2 fold and P < 0.01, as determined by a t-test.