- WBPaper00065623:38
CellRanger, DecontX, Monocle3, Louvain algorithm.
Single-cell RNA-Seq cell group 38 expressed in: Spermatocytes.
- WBPaper00061527:pqn-42_3632-pqn-42_9157
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. 8, pqn-42_3632-pqn-42_9157, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00050332:juglone_upregulated
Using the Cufflink package and CuffDiff application from Galaxy, FPKM (Fragments Per Kilobase of transcript per Million mapped reads) were calculated and tested for differential expression with a FDR score of 5%.
Transcripts that showed significantly increased expression after exposed to 38 M juglone for 3 hours.
- WBPaper00060703:nas-38(ok3407)_downregulated
A feature was classified upregulated if its FDR-corrected p-value was <= 0.05 and fold change was >= 2. Analogously, a gene was classified downregulated if its FDR-corrected p-value was <= 0.05 and fold change was <= -2.
Transcripts that showed significantly decreased expression in nas-38(ok3407) comparing to in N2.
- WBPaper00060703:nas-38(ok3407)_upregulated
A feature was classified upregulated if its FDR-corrected p-value was <= 0.05 and fold change was >= 2. Analogously, a gene was classified downregulated if its FDR-corrected p-value was <= 0.05 and fold change was <= -2.
Transcripts that showed significantly increased expression in nas-38(ok3407) comparing to in N2.
- WBPaper00061527:pqn-31-ttr-21
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. 26, pqn-31-ttr-21, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- 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: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:gst-26-pho-1_10767
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. 38, gst-26-pho-1_10767, on the genome-wide coexpression clique map for the nematode GPL200 platform.