- WBPaper00004966:beta-Naphthoflavone_induced
Differentially Expressed C. elegans CYP Genes Induced by beta-Naphthoflavone. Differential hybridization was performed using mRNA samples isolated from beta-naphthoflavone- and DMSO-treated worm populations, respectively.
- WBPaper00040412:germline-regulated_daf-16_target
All lists used an Fs:Ptab 0.01 cutoff.
Genes that were regulated by DAF-16 in response to germline loss, identified by comparing differentially expression genes between glp-1(e2141ts, 25C) vs. glp-1(e2141ts, 20C) and daf-16;glp-1(e2141ts, 25C) vs. daf-16;glp-1(e2141ts, 20C).
- WBPaper00047070:DAF-16-dependent_UV_response
Differentially expressed genes were determined by ANOVA analysis using the Partek software package.
DAF-16-dependent genes as being significantly induced (FC > 1.5; P < 0.01) following UV treatment in daf-2 mutants and more strongly induced following UV treatment in daf-2 versus daf-2;daf-16, daf-2 versus N2, and N2 versus daf-16.
- WBPaper00061527:cyp-14A4-cyp-13A4
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. 102, cyp-14A4-cyp-13A4, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00061527:cyp-33C6-cyp-35B2
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. 32, cyp-33C6-cyp-35B2, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00035479:daf-16(RNAi)_downregulated
Significance Analysis of Microarray (SAM) was performed to identify genes that were differentially regulated in each of the comparisons.For DAF-16 regulated genes, 1% median false positive discovery rate was used.
Genes upregulated in daf-2(-) compared to daf-16(-); daf-2(-)
- WBPaper00035479:daf-16(RNAi)_upregulated
Significance Analysis of Microarray (SAM) was performed to identify genes that were differentially regulated in each of the comparisons.For DAF-16 regulated genes, 1% median false positive discovery rate was used.
Genes downregulated in daf-2(-) compared to daf-16(-); daf-2(-)
- WBPaper00065623:16
CellRanger, DecontX, Monocle3, Louvain algorithm.
Single-cell RNA-Seq cell group 16 expressed in: Body wall muscle middle.