- WBPaper00061340:CEP
Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm.
Top 300 transcripts enriched in CEPDL, CEPDR, CEPVL, CEPVR according to single cell RNAseq.
- WBPaper00061651:CEP_enriched
Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched.
Transcripts enriched in CEP according to single cell RNAseq.
- WBPaper00037950:CEP-sheath-cells_Day1-adult_expressed
A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.
Genes that showed expression levels higher than the corresponding reference sample (Young adult all cell reference).
- WBPaper00037950:CEP-sheath-cells_adult_enriched
A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.
Genes significantly enriched (> 2x, FDR < 5%) in a particular cell-type versus a reference sample of all cells at the same stage.
- WBPaper00037950:CEP-sheath-cells_adult_SelectivelyEnriched
A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes.
Genes that show selective expression in a subset of cell types vs broadly expressed in many cell types. Correspond to 20% - 57% of enriched_genes for a given cell type.
- WBPaper00045380:cep-1(gk138)_upregulated_UV
ncRNAs with more than 2 fold difference in expression are considered differentially expressed
ncRNAs with significantly increased expression in cep-1(gk138) than in N2 after UV irradiation, according to RNAseq.
- WBPaper00045380:cep-1(gk138)_downregulated_normal
ncRNAs with more than 2 fold difference in expression are considered differentially expressed
ncRNAs with significantly decreased expression in cep-1(gk138) than in N2 under normal conditions, according to RNAseq.
- WBPaper00045380:cep-1(gk138)_downregulated_UV
ncRNAs with more than 2 fold difference in expression are considered differentially expressed
ncRNAs with significantly decreased expression in cep-1(gk138) than in N2 after UV irradiation, according to RNAseq.