- 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.
- WBPaper00044857:BAR-1_downregulated
Criteria used for selection of BAR-1 responsive gene targets were (1) at least a twofold change in signal response to (del)NTBAR-1 overexpression compared with control average, (2) concurrence in directional change for at least two of the three (del)NTBAR-1 induced replicates (e.g., increase or decrease of signal), and (3) an analysis of variance p-value of <=0.05.
Genes showing a statistically-significant decrease in gene expression of 2 fold or greater in response to expre ssion of delNTBAR-1 protein.
- WBPaper00044857:BAR-1_upregulated
Criteria used for selection of BAR-1 responsive gene targets were (1) at least a twofold change in signal response to (del)NTBAR-1 overexpression compared with control average, (2) concurrence in directional change for at least two of the three (del)NTBAR-1 induced replicates (e.g., increase or decrease of signal), and (3) an analysis of variance p-value of <=0.05.
Genes showing a statistically-significant increase in gene expression of 2 fold or greater in response to expre ssion of delNTBAR-1 protein.