- WBPaper00065623:44
CellRanger, DecontX, Monocle3, Louvain algorithm.
Single-cell RNA-Seq cell group 44 expressed in: Glia_1.
- WBPaper00035211:age-1_vs_N2_upregulated
SAM
Genes that showed increased expression in age-1 (mg44, m333) comparing to N2DRM. 23 (8.3%) at FDR <3%, 44 (11%) at FDR <5.5%, with expression in age-1(mg44, m333) > N2DRM.
- WBPaper00041071:spe-44_downregulated
Microarray data were analyzed by Microarray Suite 5.0 (Affymetrix) and Genomics Suite (Partek) software, using a p-value threshold of 0.05 for differential expression.
Genes with significantly decreased expression in spe-44(ok1400) comparing to N2.
- WBPaper00041071:spe-44_upregulated
Microarray data were analyzed by Microarray Suite 5.0 (Affymetrix) and Genomics Suite (Partek) software, using a p-value threshold of 0.05 for differential expression.
Genes with significantly increased expression in spe-44(ok1400) comparing to N2.
- WBPaper00064502:spe-44(fx110)_upregulated
DESeq2, fold change > 2 and a BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a cutoff for significant differen-tial expression.
Transcripts that showed significantly increased expression in spe-44(fx110) comparing to in control male animals.
- WBPaper00064502:spe-44(fx110)_downregulated
DESeq2, fold change > 2 and a BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a cutoff for significant differen-tial expression.
Transcripts that showed significantly decreased expression in spe-44(fx110) comparing to in control male animals.
- WBPaper00064502:nhr-23(kry61)\;spe-44(fx110)_downregulated
DESeq2, fold change > 2 and a BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a cutoff for significant differen-tial expression.
Transcripts that showed significantly decreased expression in nhr-23(kry61);spe-44(fx110) comparing to in control male animals.
- WBPaper00064502:nhr-23(kry61)\;spe-44(fx110)_upregulated
DESeq2, fold change > 2 and a BenjaminiHochberg multiple hypothesis-corrected P-value cutoff of 0.05 was used as a cutoff for significant differen-tial expression.
Transcripts that showed significantly increased expression in nhr-23(kry61);spe-44(fx110) comparing to in control male animals.
- WBPaper00061527:ceh-22_3981-inx-6
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. 44, ceh-22_3981-inx-6, 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.