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miRNAs that showed increased expression after exposure to graphene oxide (GO) |
The dysregulated expression of miRNAs in GO-exposed nematodes was analyzed by DESeq (an R package, a powerful tool to estimate the variance and test for differential expression). The data were extracted as up- or down-regulated miRNAs according to a cutoff of 2 fold change, and were presented in the scatter diagram after normalization. |
WBPaper00045209:graphene-oxide_upregulated
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miRNAs that showed significantly decreased expression in glp-4(bn2) at 26 centigrade, comparing to in N2 animals at 26 centigrade. |
DESeq2 q-value < 0.05. |
WBPaper00049990:glp-4(bn2)_26C_vs_N2_26C_downregulated
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MicroRNAs that showed significantly decreased expression in alg-5(ram2), comparing to in N2. |
DESeq2, Fold change > 1.5. |
WBPaper00051404:alg-5(ram2)_downregulated_miRNA
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micro RNAs that exhibit changes in expression during adulthood (p-value < = 0.05). |
Authors searched for targets with seed matches of perfect Watson-Crick base-pair complementarity to positions two-eight of the miRNAs (counting from the 5' end). In order to consider these seed matches as potential target sites, authors required a minimal cut-off for binding specificity of the remainder of the miRNA to the target. Recent evidence suggests that this is not required for function in humans, but 3' binding does occur in studies of C. elegans. Authors used the scoring algorithm from Robins et al. (2005). The binding cut-off is determined by creating a second-order Markov model of the background for the 3' UTRs. The cut off was p-value < = 0.05. |
WBPaper00028344:adult_expr_change
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Micro RNAs that showed significantly higher expression (log2fold > 2, padj < 0.01) in hermaphrodite gonad (somatic gonad plus germine) than in male gonad (somatic gonad plus germine). |
DESeq2 v1.13.8, fold change > 2, FDR < 0.01. |
WBPaper00056161:hermaphrodite_enriched_miRNA
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MicroRNAs that showed significantly increased expression after animals were exposed to 1 mg per liter multi-walled carbon nanotubes (MWCNTs) from L1 larva to young adult. |
DESeq, cut-off of 2-fold change. |
WBPaper00045019:MWCNT_upregulated
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Micro RNAs that showed significantly increased expression in day 8 adults comparing to in day 1 adults in neuron. |
Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2. |
WBPaper00066447:Day8_vs_Day1_upregulated_neuron
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miRNAs that showed significantly decreased expression in glp-4(bn2) at 26 centigrade than in 15 centigrade. |
DESeq2 q-value < 0.05. |
WBPaper00049990:glp-4(bn2)_26C_vs_15C_downregulated
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miRNAs that showed increased expression in 1 day post L4 adult hermaphrodite eat-2(ad1116) comparing to in N2. |
A fold change >= 1.5 with a minimum read count of >= 10 were used to filter the differentially expressed miRNA. The p-value cutoff was set at p <= 0.05 based on Kals Z test statistical. |
WBPaper00046156:eat-2(ad1116)_Day1_upregulated
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miRNAs that showed decreased expression in 8 days post L4 adult hermaphrodite eat-2(ad1116) comparing to in N2. |
A fold change >= 1.5 with a minimum read count of >= 10 were used to filter the differentially expressed miRNA. The p-value cutoff was set at p <= 0.05 based on Kals Z test statistical. |
WBPaper00046156:eat-2(ad1116)_Day8_downregulated
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12 hour starvation |
miRNA that showed significantly increated expression after 12 hour starvation in L4 larva stage. Fold change was calculated by dividing the higher counts per million by the lower, but adding the sign from the logFC to indicate direction. |
Authors only considered miRNA regions with at least 1 reads per-million from one of the libraries. These were tested for differential expression using the edgeR package, setting the common dispersion to 0.1 (since they did not have biological replicates) and normalizing with the TMM method. False Discovery Rates were calculated using the Benjamini & Hochberg procedure. |
WBPaper00048790:12h-starvation_upregulated_miRNA
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Micro RNAs that showed significantly decreased expression in hrpk-1(tm5522) comparing to in N2 at L4 larva stage. |
DESeq, fold change > 2, p-value <= 0.05. |
WBPaper00058673:hrpk-1(tm5522)_downregulated_miRNA_L4
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miRNA with increased expression in N2 1-day post L4 adult hermaphrodite comparing to in N2 L4 larva. |
DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively. |
WBPaper00045316:miRNA_N2_adult_vs_L4_upregulated_adult
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miRNA with decreased expression in N2 L1 larva comparing to in N2 embryo. |
DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively. |
WBPaper00045316:miRNA_N2_L1_vs_embryo_downregulated_adult
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MicroRNAs that showed significantly decreased expression in alg-1(gk214), comparing to in N2. |
DESeq2, Fold change > 1.5. |
WBPaper00051404:alg-1(gk214)_downregulated_miRNA
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MicroRNAs that showed significantly decreased expression in alg-2(ok304), comparing to in N2. |
DESeq2, Fold change > 1.5. |
WBPaper00051404:alg-2(ok304)_downregulated_miRNA
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miRNA with decreased expression in prg-1(wm161) comparing to in N2. |
DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively. |
WBPaper00045316:miRNA_prg-1_downregulated_adult
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MicroRNAs that showed significantly decreased expression in alg-5(tm1163), comparing to in N2. |
DESeq2, Fold change > 1.5. |
WBPaper00051404:alg-5(tm1163)_downregulated_miRNA
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miRNA with decreased expression in prg-1(wm161) L1 larva comparing to in prg-1(wm161) embryo. |
DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively. |
WBPaper00045316:miRNA_prg-1_L1_vs_embryo_downregulated_adult
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miRNA with increased expression in prg-1(wm161) comparing to in N2. |
DEGseq and GFOLD were used to analyze miRNAs expression. Authors chose miRNAs which had more than two-fold difference in expression (P < 0.001, q < 0.01 of Storey) from DEGseq, and miRNAs which had more than two-fold difference in expression (GFOLD score > 0 for up-regulation and GFOLD score < 0 for down-regulation) from GFOLD outcomes. Then authors obtained the intersection of up-regulated miRNAs and down-regulated miRNAs for each stage from the chosen miRNAs, respectively. |
WBPaper00045316:miRNA_prg-1_upregulated_embryo
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miRNAs with age dependent abundance in wild type animals. |
Details available in Supplementary material of the paper. Diff Exp, is the approximate ratio of expression comparing Young to Old animals (11 day difference in age). The raw p-value is for the null hypothesis that the Diff exp Ratio = 1 (based on robust inference - see supplemental information) and the associated 95% CI of the ratio. |
WBPaper00042527:age_dependent_miRNA
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Micro RNAs that showed significantly increased expression in day 8 adults comparing to in day 1 adults in body wall muscle. |
Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2. |
WBPaper00066447:Day8_vs_Day1_upregulated_BodyWallMuscle
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MicroRNAs that showed significantly decreased expression in Day 5 (5-days post-L4) vs. Day 0 (L4 larva) of adulthood mir-71(n4115) animals. |
Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method. |
WBPaper00053318:Aging_downregulated_miRNA_mir-71(n4115)
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Micro RNAs that showed significantly decreased expression in drsh-1(ok369) comparing to in N2. |
Fold change > 1.5. |
WBPaper00055896:drsh-1(ok369)_downregulated
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Micro RNAs that showed significantly decreased expression in hrpk-1(zen17) comparing to in N2 at L4 larva stage. |
DESeq, fold change > 2, p-value <= 0.05. |
WBPaper00058673:hrpk-1(zen17)_downregulated_miRNA_L4
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MicroRNAs that showed significantly decreased expression in Day 5 (5-days post-L4) vs. Day 0 (L4 larva) of adulthood N2 animals. |
Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method. |
WBPaper00053318:Aging_downregulated_miRNA_N2
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miRNAs in F1 generation up regulated by exposure to 20uM and 20mM nicotine during F0 generation. |
Statistical analysis was based on t-test for independent samples via SPSS to compare each of the nicotine treatments with control (i.e. low vs. control and high vs. control). Welch test correction was performed to account for unequal variance in each of the compared groups (control and treatment). In addition, to increase the statistical stringency, miRNAs differential expression was deemed significant only if it fulfilled two criteria: p value , 0.05 and expression changed by at least 50% relative to control. |
WBPaper00049006:nicotine_upregulated_F1
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