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Transcripts of coding 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_coding-RNA
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Single-cell RNA-Seq cell group 84_0 expressed in neuron. |
scVI 0.6.0 |
WBPaper00065841:84_0
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Transcripts enriched in ASG according to single cell RNAseq. |
Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. |
WBPaper00061651:ASG_enriched
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Single-cell RNA-Seq cell group 71_0 expressed in neuron. |
scVI 0.6.0 |
WBPaper00065841:71_0
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Transcripts that showed significantly decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage. |
DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed. |
WBPaper00048971:daf-16(mgDf50)_downregulated_L1
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Transcripts that showed significantly altered expression after 24 hour exposure to nitroguanidine (NQ). |
Multivariate permutation tests with random variance model implemented in BRB-Array Tools version 4.5 were performed to infer differentially expressed genes (DEGs). One thousand random permutations were computed per chemical class (i.e., a group of 16 arrays or samples). The confidence level of false discovery rate assessment was set at 80%, and the maximum allowed portion of false-positive genes was 10%. |
WBPaper00055899:nitroguanidine_regulated
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Genes expressed in N2. |
Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0. |
WBPaper00025141:N2_Expressed_Genes
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Genes that show significant variation due to strain by stage interaction. |
An analysis of variance (one-way ANOVA) test was used to see which genes changed significantly over developmental time, using the strain and stage of each array as the parameters. qvalue, an R-package, was used to obtain false-discovery rates (FDR). Significant genes have an FDR of less than .05. |
WBPaper00032479:CB4856vsN2_LifeStageProfile_Variation
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control(maintained under normal lab light (mostly dark, in incubators).) vs EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) at just prior to the third UVC dose (48h). |
Genes differentially expressed in control vs under EtBr treatment without UVC exposure, at the -1h timepoint. |
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_EtBr-exposed_48h
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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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Genes that showed significantly decreased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at L1 larva stage. |
BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults). |
WBPaper00053550:daf-19(m86)_downregulated_L1
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Bacteria diet: complex environmental microbiotas |
Transcripts that showed significantly decreased expression after L1 larva grew on soil microbiota at 25C for 3 days. |
N.A. |
WBPaper00056139:soil-microbiota_downregulated
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Embryonic Pan-neural Enriched Genes. |
A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets. |
WBPaper00030839:Embryo_Pan_Neuronal
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Transcripts that showed significantly increased expression in Day 8 adults comparing to in Day 1 adults in neuron cells. |
t-test, fold change > 2, p-value < 0.01. |
WBPaper00062590:Aging_upregulated_neuron
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EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) 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 without UVC exposure vs after 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:EtBr-exposed_vs_UVC-exposed_48h
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Larval Pan-neural Enriched Genes. |
A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets. |
WBPaper00030839:Larval_Pan_Neuronal
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Genes that showed significantly decreased expression after exposure to 1mg/L MWCNTs from L1 larva to young adult. |
Transcripts with false discovery rate-corrected p-values < 0.05 and fold change > 2 were defined as differentially expressed. |
WBPaper00049377:MWCNT_downregulated
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Genome-wide analysis of developmental and sex-regulated gene expression profile. |
self-organizing map |
cgc4489_group_17
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Transcripts that showed significantly decreased expression in lin-22(ot269) comparing to in N2 at L3 larva. |
Differences in gene expression were then calculated using the negative binomial test in the DESeq package (FDR = 0.1). |
WBPaper00053295:lin-22(ot269)_downregulated
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WT-Pico Pan-neural Enriched Genes, with genes found multiple times in a single dataset removed (without dups). |
To identify differentially expressed transcripts, normalized intensity values from the pan-neural data sets were compared to a reference (from all larval cells) using Significance Analysis of Microarray software (SAM). A two class unpaired analysis of the data was performed to identify neuron-enriched genes. Pan-neural enriched transcripts in the IVT and WT-Pico-derived data set were defined as 1.5X elevated vs the reference at a False Discovery Rate (FDR) = 3%. |
WBPaper00031532:Larva_Pan_Neuronal_Enriched
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Genes that showed significantly decreased expression level in rsr-2(RNAi) animals comparing to in gfp(RNAi) control. |
Fold change > 1.2 or < 0.8. |
WBPaper00042477:rsr-2(RNAi)_downregulated_TilingArray
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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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Genes enriched in neuronal miRNA-induced silencing complexes (miRISC) as detected by immunoprecipitations and microarray analysis. |
Testable genes were defined as having reliable signals in two different biological replicates using the Agilent microarray chip. Multiple probes for the same gene were removed, keeping the probe with the lowest p-value as defined by a one-tailed t-test comparing all testable probes versus probes towards a designated gene. The testable data was then supplemented with the enrichment values (as percent ranks) of a fifth replicate, from another microarray platform GPL5883 (which had a single probe for each gene), and statistical significance was re-calculate. p < 0.001 was the final cutoff. |
WBPaper00042548:miRISC_enriched
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Transcripts that showed significantly increased expression in elli-1(sam-3) comparing to in N2 animals, accordingto tiling array analysis. |
Fold change > 1.2, q-value < 0.05. |
WBPaper00050743:elli-1(sam-3)_downregulated
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Candidate daf-19 down regulated genes with a statistically significant signal variation of 1.5-fold or greater. These were identified using a class comparisons tool from BRB Array Tools. |
BRB Array Tools (version 3.3) was subsequently used to identify genes with a statistically significant variation in expression when comparing between the two classes defined in this study. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically different. Genes with a signal variation of 1.5-fold or greater were selectively identified for use in all subsequent experiments. To reduce the chances of false discoveries, a class comparison test was conducted using a multivariate permutation test with the confidence level of 97%. |
WBPaper00039866:ClassComp_daf-19_downregulated
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Genes that showed significantly decreased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at 3-fold embryo stage. |
BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults). |
WBPaper00053550:daf-19(m86)_downregulated_3-fold-embryo
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Candidate daf-19 down regulated genes with a statistically significant signal variation of 1.5-fold or greater. These were identified using a Significance Analysis of Microarrays (SAM). |
Lists of genes were generated using SAM (version 2.2) with a false discovery rate (FDR) of less than or equal to 5% (Q-value <= 5%). Twenty-seven repeated runs of SAM were performed using variable random seed numbers for each run. During each run of SAM, 100 permutations were performed. Genes (n =129 downregulated, n = 1 upregulated) appearing in at least 80% of all twenty-seven runs of SAM were further considered for signal variation filtering, which was used to selectively identify genes with a 1.5-fold or greater variation between the two genetic conditions used for comparison. |
WBPaper00039866:SAM_daf-19_downregulated
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Genes whose transcripts exhibited >= 2 fold change in expression between wild-type and adr-2(ok735) neural cells. |
DESeq2. Genes with a greater than 2-fold change in expression were reported. |
WBPaper00053094:adr-2(ok735)_neuron_upregulated
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Top 300 transcripts enriched in ASGL, ASGR according to single cell RNAseq. |
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. |
WBPaper00061340:ASG
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