WBPaper00032454:IR_upregulated

To identify differentially expressed genes, gene expression intensity was compared using a moderated t-test and a Bayes smoothing approach developed for a low number of replicates. Genes up-regulated following ionizing radiation (IR) treatment.

WBPaper00045401:N.parisii_64h_downregulated

Differentially expressed transcripts were identified using the edgeR Bioconductor package (Empirical analysis of digital gene expression data in R, v 3.0.8). FDR cutoff was set to < 0.05, which yielded lists of genes with > 4-fold difference in expression. Genes that showed significantly decreased expression 64 hours after infection by Nematocida parisii in fer-15(b26); fem-1(hc17), according to RNAseq.

WBPaper00045401:N.parisii_64h_upregulated

Differentially expressed transcripts were identified using the edgeR Bioconductor package (Empirical analysis of digital gene expression data in R, v 3.0.8). FDR cutoff was set to < 0.05, which yielded lists of genes with > 4-fold difference in expression. Genes that showed significantly increased expression 64 hours after infection by Nematocida parisii in fer-15(b26); fem-1(hc17), according to RNAseq.

WBPaper00061527:T24D1.3-egg-1

All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform. Coexpression clique No. 64, T24D1.3-egg-1, on the genome-wide coexpression clique map for the nematode GPL200 platform.

WBPaper00061527:his-46_959-his-64

All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform. Coexpression clique No. 233, his-46_959-his-64, on the genome-wide coexpression clique map for the nematode GPL200 platform.

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.