- WBPaper00065623:36
CellRanger, DecontX, Monocle3, Louvain algorithm.
Single-cell RNA-Seq cell group 36 expressed in: Spermatheca bag proximal.
- WBPaper00061527:Y39B6A.3-pfd-6
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. 74, Y39B6A.3-pfd-6, on the genome-wide coexpression clique map for the nematode GPL200 platform.
- WBPaper00062056:lin-36(we31)_downregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly decreased expression in lin-36(we31) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00062056:lin-36(we36)_upregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly increased expression in lin-36(we36) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00038118:aak-2(gt33)_downregulated
Audic-Claverie test of statistical significance using normalized read frequencies (i.e. Normalized number of reads per gene = number of reads mapped to a gene * the read length (36 bases)/the gene length/total number of reads in the library) of commonly identified genes. Genes that had p-values less than 0.01 and log2 expression level ratios greater than 0.7 (Minimum of ~1.5 difference) for every comparison were selected as differentially expressed.
Significantly down-regulated genes in unstressed aak-2(gt33) relative to N2.
- WBPaper00062056:lin-36(n766)_downregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly decreased expression in lin-36(n766) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00062056:lin-36(n766)_upregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly increased expression in lin-36(n766) comparing to in N2 animals at starved L1 larva stage.