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Transcripts that showed significantly increased expression in ngn-1(ok2200) embryos comparing to in N2. |
DESeq2 ver.3.4.1 |
WBPaper00059537:ngn-1(ok2200)_upregulated
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spermatogenesis-enriched |
Comparisons were made between genotypes by subtracting the mean log value of one ratio from another, and the significance of the difference was evaluated using Student t-test for two populations. For the fem-3(gf) versus fem-1(lf) direct comparison, authors performed the same analysis, except they used a Students t-test for one population. Author chose a combination of a twofold difference with a t value exceeding 99% confidence (P < 0.01), because these criteria allowed the inclusion of essentially all genes that had previously been identified as germline-enriched in a wt/glp-4 hermaphrodite comparison. Additionally, requiring a twofold difference reduced false positives, as the number of genes with two-fold difference and a P<0.01 only included ~100 genes more than with P < 0.001, and almost all genes showed germline expression by in situ hybridization. |
[cgc6390]:spermatogenesis-enriched
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Transcripts that showed significantly decreased expression in mrps-5(RNAi) animals comparing to animals injected with empty vector. |
Differential expression was assessed using a Partial least-squares discriminant analysis (PLS-DA) using mixomics setting a variable of importance (VIP) score of greater than 1 as significant. |
WBPaper00059328:mrps-5(RNAi)_downregulated_mRNA
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Transcripts that showed significantly altered expression in olrn-1(ums9) comparing to in N2 animals. |
The Ballgown package from the Bioconductor software suite (version 3.8) was used to run a custom R script in R console(R Version 3.5) to analyze the differential gene expression, visualize the data, and perform statistical tests for differential expressionwith multiple test correction. A gene was considered to be differentially regulated if its fold change versus wild-type was greater thantwo, the adjusted p value was less than 0.05, and its RPKM was greater than one. |
WBPaper00059567:olrn-1(ums9)_regulated
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Transcripts that showed significantly decreased expression after synchronized L4 staged worms were treated with 10 mM caffeine at 25C for 72 hours. |
DESeq2 |
WBPaper00067717:caffeine_downregulated
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Transcripts of noncoding genes that showed significantly decreased expression in muscle. |
DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed. |
WBPaper00062325:muscle_depleted_noncoding-RNA
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Genome-wide analysis of developmental and sex-regulated gene expression profile. |
self-organizing map |
cgc4489_group_16
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