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Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014. |
N.A. |
WBPaper00026929:sir-2.1_overexpression_regulated
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Significantly upregulated genes from cyc-1(RNAi) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips. |
SAM algorithm with an FDR < 0.1. |
WBPaper00033065:cyc-1(RNAi)_upregulated
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Genes identified as up-regulated at a 5% false discovery rate through RNAseq experiments with three tatn-1(qd182) and three N2 RNA samples. |
ANOVA with FDR <= 0.05. |
WBPaper00044656:tatn-1(qd182)_upregulated
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Transcripts that showed significantly increased 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)_upregulated_mRNA
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mRNAs that were significantly enriched in the AIN-2 immunoprecipitation samples, compared to the control total mRNAs in the input extracts (p < 0.01). |
Signals from replicates of total worm lysates from wt and strains containing the ain-2::gfp or the ain-2 promoter::gfp transgene were mean normalized and averaged respectively to generate standard profiles of gene expression in these worm strains. Authors then calculated the ratio of signal of each gene from each IP sample to the standard gene expression profile of the corresponding worm strain. Based on this ratio, a percentile rank of each gene relative to all genes in each IP replicate was calculated. The percentile ranks in the three replicates of each IP were averaged. Student t test was utilized to determine if the average percentile ranks of enrichment of individual genes were significantly higher (p value) than the mean enrichment of all genes in the IP samples. To determine the AIN-1 or AIN-2 associated genes, we used the following criteria: (1) average percentile ranks of enrichment is greater than the mean enrichment of all genes in AIN-1 or AIN-2 IP with p < 0.01; (2) average signal in AIN-1 or AIN-2 IP replicates is greater than the background signal (including 2X standard deviation (SD)) (Background signal and SD were calculated based on signals from empty spots on each microarray); (3) criteria 1 is not be satisfied for the same gene in the corresponding control IP. |
WBPaper00031252:AIN-2_IP_enriched
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Transcripts that showed significantly increased expression in mrps-5(RNAi) comparing to in control animals. |
Fold change > 4, p-value < 0.01 |
WBPaper00056330:mrps-5(RNAi)_upregulated
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Bacteria Diet: L. plantarum with pdxH mutant vs. L. plantarum |
Transcripts that showed significantly increased expression in N2 animals fed with L. plantarum with pdxH mutant, comparing to in N2 animals fed with L. plantarum. |
GFold3, logFC < -1 or > 1. |
WBPaper00066703:L.plantarum-pdxH_upregulated
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Transcripts that showed significantly increased expression in cco-1/cox-5B(RNAi) animals comparings to animals injected with vector control. |
LimmaVoom. The genes with a BenjaminiHochbergadjusted P value < 0.05 were defined as statistically significant. Genes whose expressions were significantly upregulated with log2FC > 0.393. |
WBPaper00064637:cox-5B(RNAi)_upregulated
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Genome-wide analysis of developmental and sex-regulated gene expression profile. |
self-organizing map |
cgc4489_group_13
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Coexpression clique No. 282, srj-21-srh-32, on the genome-wide coexpression clique map for the nematode GPL200 platform. |
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. |
WBPaper00061527:srj-21-srh-32
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Transcripts that showed significantly increased expression in ADL neurons of qui-1(db104) comparing to in N2 at day 1 adult stage. |
tximport 1.14.2 and DEseq2 1.26.0. Fold change > 2, FDR < 0.05. |
WBPaper00062520:qui-1(db104)_upregulated
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Single-cell RNA-Seq cell group 81_0 expressed in neuron. |
scVI 0.6.0 |
WBPaper00065841:81_0
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Genes enriched in body wall muscle AIN-2 miRISCs. Pmyo-3-ain-2-gfp IP was performed in mixed stage worms. |
Enrichment values are expressed as mean percent rank. The p value was computed by comparing all enrichment values for a given transcript to all enrichment values of all transcripts by a one-tailed t test. Significantly enriched genes are those with p value < 0.01. |
WBPaper00040985:AIN-2_asynchronous_muscle
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