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Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells. |
DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. |
WBPaper00060811:L1_vs_adult_upregulated_neural
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Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. |
DESeq. False discovry rate (FDR) < 0.1. |
WBPaper00048988:neuron_expressed
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adult vs dauer larva |
Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C. |
N.A. |
WBPaper00050488:adult_vs_dauer_regulated_N2_20C
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Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology. |
DESEQ2, fold change > 2 and FDR < 0.01. |
WBPaper00062103:neuron_enriched
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Genome-wide analysis of developmental and sex-regulated gene expression profile. |
self-organizing map |
cgc4489_group_18
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Bacteria: B.subtilis |
Transcripts that showed significantly decreased expression when animals were fed by probiotic bacteria strain B.subtilis PXN21 comparing to animals fed with OP50 from L1 till day 1 adult. |
edgeR 3.16.5, FDR < 0.05, fold change > 2. |
WBPaper00059117:B.subtilis_downregulated
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Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00066594:ilc-17.1(syb5296)_upregulated
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Transcripts that showed significantly increased expression in dpy-21(e428) comparing to in N2 during L3 stage. |
DESeq v1.6.3. Fold change > 1.5. |
WBPaper00050370:dpy-21(e428)_L3_upregulated
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Transcripts that showed significantly increased expression in whole animal day 1 N2 adults comparing to in whole animal day 8 N2 adults. |
DESeq2, FDR < 0.05, fold change > 2. |
WBPaper00066978:Day1Adult_vs_Day8Adult_upregulated_neuron
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Transcripts that showed differential expression in dauer mir-34(gk437) vs dauer mir-34(OverExpression) animals at 20C. |
N.A. |
WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_dauer_20C
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male soma-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]:male_soma-enriched
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control(maintained under normal lab light (mostly dark, in incubators).) vs UVC-EtBr-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total) and exposed to EtBr (5ug/mL in agar).) at just prior to the third UVC dose (48h). |
Genes differentially expressed in control vs after UVC exposure and EtBr treatment at the -1h timepoint (just prior to the third UVC dose (48h)). |
Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. |
WBPaper00041939:control_vs_UVC-EtBr-exposed_48h
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UVC-EtBr-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total) and exposed to EtBr (5ug/mL in agar).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at just prior to the third UVC dose (48h). |
Genes differentially expressed under EtBr treatment and UVC exposure vs under UVC exposure but without EtBr treatment at the -1h timepoint (just prior to the third UVC dose (48h)). |
Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. |
WBPaper00041939:UVC-EtBr-exposed_vs_UVC-exposed_48h
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Transcripts that showed differential expression in dauer N2 vs dauer mir-34(gk437) animals at 20C. |
N.A. |
WBPaper00050488:N2_vs_mir-34(gk437)_regulated_dauer_20C
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Fungi infection: Drechmeria coniospora |
Genes with decreased expression after 12 hours of infection by D.coniospora Fold changes shown are pathogen vs OP50. |
For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated. |
WBPaper00038438:D.coniospora_12hr_downregulated_RNAseq
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Transcripts that showed significantly decreased expression in unc-70(cas983) comparing to in N2 at L1 larva stage. |
DESeq2, fold change >= 2, FDR <= 0.05 |
WBPaper00057041:unc-70(cas983)_downregulated
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mRNAs that were significantly enriched in the AIN-1 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-1_IP_enriched
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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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Transcripts that showed significantly increased expression in mex-1(or286) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. |
RPKM fold change > 2. |
WBPaper00058598:mex-1(or286)_upregulated
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Transcripts that showed significantly increased expression in mex-3(eu149) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. |
RPKM fold change > 2. |
WBPaper00058598:mex-3(eu149)_upregulated
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Fungi infection: Harposporium sp. |
Genes with increased expression after 24 hours of infection by Harposporium Fold changes shown are pathogen vs OP50. |
For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated. |
WBPaper00038438:Harposporium_24hr_upregulated_RNAseq
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Transcripts that showed significantly increased expression in sensory neuron (labeled by iaIs25[Pgcy-37::GFP + unc-119(+)]) comparing to in whole worm. |
Fold change > 2, p-value < 0.05. |
WBPaper00060661:sensory-neuron_enriched
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Transcripts that showed significantly decreased expression in CB4856 animals growing in 15mg per mL doxycycline from L1 to L4 larva stage. |
edgeR (version 3.24.3), fold change > 4, FDR < 0.01. |
WBPaper00062456:doxycycline_downregulated_CB4856_transcript
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Transcripts that showed significantly increased expression in natural variant RC301(that showed resistance towards bacteria infection) vs. natural variant DA650, after 4 hour of infection by P. aeruginosa PA14. |
Fold change > 2, p-value < 0.05. |
WBPaper00050712:RC301_vs_DA650_4h-PA_upregulated
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Genes with variation in expression level across conditions (control, 25C, High-pH-Salt, Liquid, infection). |
two-way ANOVA |
WBPaper00041174:environmental
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Genes with variation in expression level across genotypes (AB2, CB4856, RC301, CB4857, N2, HC445). |
two-way ANOVA |
WBPaper00041174:genotypic
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Genes with significant variation across both genotypes and environments. Genotypes |
two-way ANOVA |
WBPaper00041174:genotypic_and_environmental
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Transcripts that showed significantly decreased expression in swsn-1(os22ts) comparing to in N2 animals at young adult worms. |
DESeq2, FDR<0.05 and fold-change 2. (Threshold set by WormBase curator.) |
WBPaper00060764:swsn-1(os22ts)_downregulated
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Genome-wide analysis of developmental and sex-regulated gene expression profile. |
self-organizing map |
cgc4489_group_15
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Transcripts depleted at neuron synapses (enriched at the somatic fragments) by comparing presynaptic and somatic cell fragments labeled with different protein markers and sorted by FACS. |
DESeq2, FDR < 0.05 |
WBPaper00059027:neuron-synapses_depleted
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