- WBPaper00065623:66
CellRanger, DecontX, Monocle3, Louvain algorithm.
Single-cell RNA-Seq cell group 66 expressed in: Hypodermis head.
- WBPaper00059664:srbc-48(ac23)_downregulated
DESeq2, FDR <0.05, fold change > 2.
Transcripts that showed significantly decreased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.
- WBPaper00059664:srbc-48(ac23)_upregulated
DESeq2, FDR <0.05, fold change > 2.
Transcripts that showed significantly increased expression in srbc-48(ac23);kyIs262;fer-1(b232ts) comparing to in kyIs262;fer-1(b232ts), 24h after infection with P.aeruginosa.
- WBPaper00040998:nhr-66_regulated
Pair-wise significance testing (mutant vs. wild-type) was performed using the Bioconductor package limma and p-values were initially corrected for multiple testing using the false discovery rate (FDR) method of Benjamini and Hochberg. Criteria for differential expression was set by employing log2(ratio) >= 0.848 and p-value < 0.001.
Differentially expressed genes in nhr-66(ok940) compared to wild-type animals using microarray analysis.
- WBPaper00061527:183712_at-srbc-74_8864
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. 144, 183712_at-srbc-74_8864, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00061527:atad-3-mpst-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. 66, atad-3-mpst-1, on the genome-wide coexpression clique map for the nematode GPL200 platform.