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Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
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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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mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis. |
Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05. |
WBPaper00045420:fertilization_downregulated_transcript
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Heat shock: 35C for 1 hour. |
Transcripts that showed significantly increased expression immediately after 1-day post L4 adult hermaphrodite endu-2(tm4977) animals were exposed to 35C for 1 hour. |
The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01. |
WBPaper00065749:Heat-Shock_upregulated_endu-2(tm4977)
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Heat shock: 35C for 1 hour. |
Transcripts that showed significantly increased expression immediately after 1-day post L4 adult hermaphrodite N2 animals were exposed to 35C for 1 hour. |
The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01. |
WBPaper00065749:Heat-Shock_upregulated_N2
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Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 hours at 24 centigrade). |
For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR). |
WBPaper00040858:eQTL_age_regulated_developing
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Genes with expression level regulated by genotype (N2 vs CB4856) at L3 larva and Late reproduction stage (96 hours at 24 centigrade). |
For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR). |
WBPaper00040858:eQTL_regulated_developing
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Transcripts that showed significantly increased expression in animal with pgph-2 overepxreesion [pgph-2p-pgph-2; myo-2p-mcherry] in glucose excess condition. |
Genes with anadjusted P-value <= 0.05 found by DESeq2 were assigned as differentially expressed. |
WBPaper00065926:pgph-2(overepxreesion)_upregulated_glucose
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Heat shock: 34C 30min. |
Transcripts that showed significantly increased expression in L2 larva stage C. elegans animals after incubated in a 34C water bath for 30min. |
DESeq2 v 1.18.1, fold change > 2, FDR < 0.01. |
WBPaper00058955:heatshock_upregulated_CE
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Transcripts of coding genes that showed significantly increased 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_enriched_coding-RNA
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20C vs 25C |
Transcripts that showed differential expression in 20C vs 25C in mir-34(OverExpression) animals at adult stage. |
N.A. |
WBPaper00050488:20C_vs_25C_regulated_mir-34(OverExpression)_adult
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Bacteria infection: Serratia marcescens |
Genes with increased expression after 24 hours of infection by S.marcescens 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:S.marcescens_24hr_upregulated_TilingArray
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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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Transcripts that showed significantly decreased 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_downregulated_neuron
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Temprature shift to 28C for 48 hours. |
Transcripts that showed significantly increased expression after animals were exposed to 28C temperature for 48 hours. |
Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control. |
WBPaper00061341:28C_48h_upregulated
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Genes upregulated in daf-2(-) compared to daf-16(-); daf-2(-) |
Significance Analysis of Microarray (SAM) was performed to identify genes that were differentially regulated in each of the comparisons.For DAF-16 regulated genes, 1% median false positive discovery rate was used. |
WBPaper00035479:daf-16(RNAi)_downregulated
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Genes that showed significant differential expressed between control and 150 mg\/L Atrazine treatment. |
t-test, p < 0.05. |
WBPaper00036123:Atrazine_regulated
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Bacteria infection: Photorhabdus luminescens |
Genes with increased expression after 24 hours of infection by P.lumniescens 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:P.lumniescens_24hr_upregulated_TilingArray
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Bacteria: Pseudomonas donghuensis HYS |
Transcripts that showed significantly increased expression after 24 hours of infection by Pseudomonas donghuensis HYS, comparing to control animals exposed to OP50. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00068216:HYS_vs_OP50_upregulated
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Bacteria: Pseudomonas donghuensis HYS |
Transcripts that showed significantly decreased expression after 24 hours of infection by Pseudomonas donghuensis HYS with deletion of ferric uptake regulator (FUR), comparing to control animals exposed to HYS. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00068216:FUR_vs_HYS_downregulated
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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 spn-4(tm291) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. |
RPKM fold change > 2. |
WBPaper00058598:spn-4(tm291)_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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Heat Shock: 35C 4 hours at L4 larva stage. |
Transcripts that showed significantly increased expression after L4 larva N2 animals were heat stressed at 35C for 4 hours |
DESeq2 |
WBPaper00057154:HeatShock_upregulated_mRNA
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Genome-wide analysis of developmental and sex-regulated gene expression profile. |
self-organizing map |
cgc4489_group_5
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Transcripts that interact with endogenous EGL-43-GFP at L3 larva stage according to CHIP-Seq analysis. |
N.A. |
WBPaper00059471:EGL-43_interacting
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Transcripts significantly enriched in AVK neurons comparing to all cell types at L1 larva stage. |
edgeR, FDR < 0.001, fold change > 2. |
WBPaper00055565:AVK_enriched
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Transcripts that showed differential expression in adult mir-34(gk437) vs adult mir-34(OverExpression) animals at 20C. |
N.A. |
WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_adult_20C
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Transcripts that showed differential expression in adult mir-34(OverExpression) vs adult N2 animals at 20C. |
N.A. |
WBPaper00050488:mir-34(OverExpression)_vs_N2_regulated_adult_20C
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Transcipts that showed significantly increased expression in old (days 24, 14, and 9 of adulthood) octr-1(ok371) comparing to in N2 at 15C. |
DESeq2 v1.31.16, fold change > 2, FDR < 0.05 |
WBPaper00068082:octr-1(ok371)_upregulated_old_15C
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