WBPaper00061210:huIs179_upregulated

Differential gene expression analysis was done with DESeq2 R-package using an FDR based on adjusted P < 0.05. (The threshold was reset from FDR < 0.1 to FDR < 0.05 by WormBase curator.) Transcripts that showed significantly increased expression in Q neuroblast descendant cells expressing a constitutively active, N terminally truncated form of BAR-1 (beta-catenin) (del-N-BAR-1 Q) (huIs179).

WBPaper00061210:huIs179_downregulated

Differential gene expression analysis was done with DESeq2 R-package using an FDR based on adjusted P < 0.05. (The threshold was reset from FDR < 0.1 to FDR < 0.05 by WormBase curator.) Transcripts that showed significantly decreased expression in Q neuroblast descendant cells expressing a constitutively active, N terminally truncated form of BAR-1 (beta-catenin) (del-N-BAR-1 Q) (huIs179).

WBPaper00045257:bar-1(ga80)_upregulated

All statistical analyses were performed using the statistical programming language R (version 2.13.1 x 64). A linear model was used to determine the effect and significance of the genotype on the expression levels (probe intensity + genotype + error). Using permutations of the original data in the same linear model, authors determined thresholds adjusted for multiple testing (FDR 0.05: -log10(p) > 2; FDR 0.01: -log10(p) > 3). To correct for the developmental difference between bar-1(ga80) and N2 authors used the developmental gene expression data from Snoek et al. (2014) together with the gene expression data generated for this study (bar-1(ga80) vs. N2) in one linear model (probe intensity, sample age + genotype + error). The intensities were corrected for batch effect and for sample age authors used an age of 44 hours for the bar-1(ga80) samples (as estimated), and 48 hours for the N2 samples. Genes that showed increased expression in bar-1(ga80) animal comparing to in N2.

WBPaper00045257:bar-1(ga80)_downregulated

All statistical analyses were performed using the statistical programming language R (version 2.13.1 x 64). A linear model was used to determine the effect and significance of the genotype on the expression levels (probe intensity + genotype + error). Using permutations of the original data in the same linear model, authors determined thresholds adjusted for multiple testing (FDR 0.05: -log10(p) > 2; FDR 0.01: -log10(p) > 3). To correct for the developmental difference between bar-1(ga80) and N2 authors used the developmental gene expression data from Snoek et al. (2014) together with the gene expression data generated for this study (bar-1(ga80) vs. N2) in one linear model (probe intensity, sample age + genotype + error). The intensities were corrected for batch effect and for sample age authors used an age of 44 hours for the bar-1(ga80) samples (as estimated), and 48 hours for the N2 samples. Genes that showed decreased expression in bar-1(ga80) animal comparing to in N2.

WBPaper00005124:progesterone_10-5M_regulated

The normalized values used were: G/R ratio > 2.6 for up-regulation and G/R ratio < 0.38 for down-regulation, which corresponds to 1.39 and -1.39 log(base2) G/R ratio, respectively. Genes up or down regulated by 10e-05M of progesterone. The normalized values used were G/R ratio > 2.6 for up-regulation and G/R ratio < 0.38 for down-regulation, which corresponds to 1.39 and -1.39 log(base2) G/R ratio, respectively.

WBPaper00005124:cholesterol_10-9M_regulated

The normalized values used were: G/R ratio > 2.6 for up-regulation and G/R ratio < 0.38 for down-regulation, which corresponds to 1.39 and -1.39 log(base2) G/R ratio, respectively. Genes up or down regulated by 10e-09M of cholesterol . The normalized values used were G/R ratio > 2.6 for up-regulation and G/R ratio < 0.38 for down-regulation, which corresponds to 1.39 and -1.39 log(base2) G/R ratio, respectively.

WBPaper00005124:progesterone_10-9M_regulated

The normalized values used were: G/R ratio > 2.6 for up-regulation and G/R ratio < 0.38 for down-regulation, which corresponds to 1.39 and -1.39 log(base2) G/R ratio, respectively. Genes up or down regulated by 10e-09M of progesterone. The normalized values used were G/R ratio > 2.6 for up-regulation and G/R ratio < 0.38 for down-regulation, which corresponds to 1.39 and -1.39 log(base2) G/R ratio, respectively.

WBPaper00005124:progesterone_10-7M_regulated

The normalized values used were: G/R ratio > 2.6 for up-regulation and G/R ratio < 0.38 for down-regulation, which corresponds to 1.39 and -1.39 log(base2) G/R ratio, respectively. Genes up or down regulated by 10e-07M of progesterone. The normalized values used were G/R ratio > 2.6 for up-regulation and G/R ratio < 0.38 for down-regulation, which corresponds to 1.39 and -1.39 log(base2) G/R ratio, respectively.

WBPaper00005124:testosterone_10-9M_regulated

The normalized values used were: G/R ratio > 2.6 for up-regulation and G/R ratio < 0.38 for down-regulation, which corresponds to 1.39 and -1.39 log(base2) G/R ratio, respectively. Genes up or down regulated by 10e-09M of testosterone. The normalized values used were G/R ratio > 2.6 for up-regulation and G/R ratio < 0.38 for down-regulation, which corresponds to 1.39 and -1.39 log(base2) G/R ratio, respectively.

WBPaper00005124:estrogen_10-5M_regulated

The normalized values used were: G/R ratio > 2.6 for up-regulation and G/R ratio < 0.38 for down-regulation, which corresponds to 1.39 and -1.39 log(base2) G/R ratio, respectively. Genes up or down regulated by 10e-05M of estrogen. The normalized values used were G/R ratio > 2.6 for up-regulation and G/R ratio < 0.38 for down-regulation, which corresponds to 1.39 and -1.39 log(base2) G/R ratio, respectively.