- WBPaper00065623:38
CellRanger, DecontX, Monocle3, Louvain algorithm.
Single-cell RNA-Seq cell group 38 expressed in: Spermatocytes.
- 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: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.
- WBPaper00036383:ash-2_L3_regulated
One-class analysis in significance analysis of microarrays (SAM)38 was performed comparing empty vector to ash-2 RNAi using a 5% false discovery rate (FDR). Resulting SAM lists of genes regulated by ASH-2 were compared for genes that were specifically changed in N2, but not in glp-1(e2141ts) mutant worms. A complete linkage hierarchical clustering was performed using Gene Cluster 3.0. Clustering results were analysed further with Java Treeview40. GOstat41 was used to identify overrepresented gene ontology categories in the list of ASH-2 regulated genes that were dependent on the presence of the germline.
Genes that change expression level at L3 larva stage after ash-2 RNAi.
- WBPaper00036383:ash-2_Day8_regulated
One-class analysis in significance analysis of microarrays (SAM)38 was performed comparing empty vector to ash-2 RNAi using a 5% false discovery rate (FDR). Resulting SAM lists of genes regulated by ASH-2 were compared for genes that were specifically changed in N2, but not in glp-1(e2141ts) mutant worms. A complete linkage hierarchical clustering was performed using Gene Cluster 3.0. Clustering results were analysed further with Java Treeview40. GOstat41 was used to identify overrepresented gene ontology categories in the list of ASH-2 regulated genes that were dependent on the presence of the germline.
Genes that change expression level at day 8 adult stage after ash-2 RNAi.