- WBPaper00065623:54
CellRanger, DecontX, Monocle3, Louvain algorithm.
Single-cell RNA-Seq cell group 54 expressed in: Spermatheca-Uterine junction.
- WBPaper00038427:lin-54_embryo_changed
To determine differentially expressed genes between wild-type and mutants, moderated T Statistics in limma was used with p-value <= 0.01, fold change >= 1.5.
Genes with changed expression in lin-54(n2290) embryo.
- WBPaper00038427:lin-54_germline_changed
To determine differentially expressed genes between wild-type and mutants, moderated T Statistics in limma was used with p-value <= 0.01, fold change >= 1.5.
Genes with changed expression in lin-54(n3423) germline.
- WBPaper00053289:DREAM-target
N.A.
Transcripts with promoter regions binding DREAM protein complex, according to ChIP-seq of E2F-DP (DPL-1 and EFL-1) and MuvB (LIN-9, LIN-37, LIN-52, and LIN-54) of N2 late embryo.
- WBPaper00046499:AMPK_regulated
Genes were tested for differential expression between each mutant strain and wild-type using edgeRs glm method. Briefly, negative binomial models were fitted and dispersion estimates obtained. These were then used to calculate average levels of change between conditions and determine differential expression, using the generalized linear model likelihood ratio test. For each comparison, genes with less than 5 CPM were filtered and those with at least 50% change and False Discovery Rate (FDR) of 1% or less were considered differentially expressed.
mRNAs that showed differential expression in activated AAK-2(uthIs202[aak-2 (intron 1)::aak-2(aa1-aa321)::Tomato::unc-54 3'UTR + rol-6(su1006)]), activiated CRTC-1 (uthEx222[crtc-1p::crtc-1 cDNA (S76S, S179A)::tdTomato::unc-54 3'UTR + rol-6(su1006)]), or AAK-2;CRTC-1 comparing to in N2.
- WBPaper00061527:pqn-54-abu-9
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. 298, pqn-54-abu-9, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00061527:mrpl-54-lbp-4
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. 151, mrpl-54-lbp-4, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00061527:kle-2_4298-vrk-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. 54, kle-2_4298-vrk-1, on the genome-wide coexpression clique map for the nematode GPL200 platform.