- WBPaper00058955:heatshock_upregulated_CE
DESeq2 v 1.18.1, fold change > 2, FDR < 0.01.
Transcripts that showed significantly increased expression in L2 larva stage C. elegans animals after incubated in a 34C water bath for 30min.
- WBPaper00065623:32
CellRanger, DecontX, Monocle3, Louvain algorithm.
Single-cell RNA-Seq cell group 32 expressed in: Seam cells (bus+) and excretory duct subpopulation.
- WBPaper00059477:lin-32(RNAi)_regulated
Both edgeR FDR and DESeq2 FDR < 0.05 required for a gene to be considered differentially expressed.
Transcripts that showed significant change of expression in lin-32(RNAi) comparing to N2 animals injected with vector control.
- WBPaper00052959:hsf-1(RNAi)_regulated_miRNA_HS-dependent
The Benjamini-Hochberg correction for multiple testing was then used to determine significantly altered miRNAs between each treatment condition. Micro RNAs with q-value < 0.05 was considered differentially expressed.
MicroRNAs that showed significantly altered expression in hsf-1(+);+HS vs hsf-1(RNAi);+HS. Worms remained on RNAi plates until the L4 larval-stage before being heat shocked by submerging plates in a 33C water bath for 30 minutes.
- WBPaper00058955:heatshock_upregulated_CBG
DESeq2 v 1.18.1, fold change > 2, FDR < 0.01.
Transcripts that showed significantly increased expression in L2 larva stage C. briggsae animals after incubated in a 34C water bath for 30min.
- WBPaper00061527:bath-38-Y105E8B.7
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. 266, bath-38-Y105E8B.7, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00061527:ima-1_20458-bath-41
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. 271, ima-1_20458-bath-41, 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.
- WBPaper00061527:srj-21-srh-32
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. 282, srj-21-srh-32, on the genome-wide coexpression clique map for the nematode GPL200 platform.