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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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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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TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood. |
SAM |
WBPaper00031040:TGF-beta_adult_upregulated
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Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals. |
Fold change > 2, FDR < 0.01. |
WBPaper00065993:glp-1(e2141)_upregulated
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Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. |
Cufflinks FPKM value >=1. |
WBPaper00050990:intestine_expressed
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Genes with expression level regulated by genotype (N2 vs CB4856) and age at old adults stage (214 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_aging
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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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Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals. |
Fold change > 2, FDR < 0.05 |
WBPaper00064088:Day-1-adult_vs_L4_upregulated_daf-16(mu86);glp-1(e2141)
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Genes with expression level regulated by genotype (N2 vs CB4856) at old adults stage (214 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_aging
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Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. |
Fold change > 2, FDR < 0.05 |
WBPaper00064088:Day-1-adult_vs_L4_upregulated_fem-3(q20)
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Transcripts that showed significantly increased expression in day 1 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. |
Fold change > 2, FDR < 0.05 |
WBPaper00064088:Day-1-adult_vs_L4_upregulated_glp-1(e2141)
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Transcripts that showed significantly increased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. |
Fold change > 2, FDR < 0.05 |
WBPaper00064088:Day-3-adult_vs_L4_upregulated_fem-3(q20)
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Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684) |
To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs. |
WBPaper00047131:daf-2(e1370)_upregulated_hel-1(gk148684)-background
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Genes that showed significantly increased expression in daf-2(e1370) comparing to in N2. |
To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs. |
WBPaper00047131:daf-2(e1370)_upregulated_N2-background
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Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage. |
DESeq2 version 1.22.2, p < 0.05 |
WBPaper00064716:paraquat_downregulated
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Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals. |
Sleuth |
WBPaper00051558:aging_regulated
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Transcripts that showed significantly altered expression after 24 hour exposure to stavudine (d4T) starting at L1 lava stage. |
DESeq |
WBPaper00053302:stavudine_24h_regulated
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25C vs. 20C |
Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite N2 grown at 25C, comparing to in N2 animals grown at 20C. |
CuffDiff, fold change > 2. |
WBPaper00065096:25C_vs_20C_upregulated
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Transcripts that showed significantly increased expression in 10-days post L4 adult hermaphrodite N2 grown at 20C, comparing to in 1-day post L4 adult hermaphrodite N2 animals grown at 20C. |
CuffDiff, fold change > 2. |
WBPaper00065096:Day10_vs_Day1_upregulated
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Transcripts that showed significantly increased expression in 1-day post L4 adult hermaphrodite npr-8(ok1439) animals grown at 20C, comparing to in N2 animals. |
CuffDiff, fold change > 2. |
WBPaper00065096:npr-8(ok1439)_upregulated_Day1_20C
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Transcripts that showed significantly increased expression in animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection. |
DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1. |
WBPaper00066146:germline-inx-14(RNAi)_upregulated_PA14
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Bacteria diet: Lb.rhamnosus |
Transcripts that showed significantly decreased expression in animals fed with heterofermentative LAB Lb. rhamnosus, comparing to animals fed with OP50 from day 1 to day 5 adult stage. |
fold change > 2 and p value < 0.05 by Students t- test. |
WBPaper00065392:Lb.rhamnosus_downregulated
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Transcripts that showed significantly decreased expression in daf-2(e1370); daf-18(nr2037) comparing to in daf-2(e1370) animals. |
Differentially expressed genes (fold change > 2 and adjusted p value < 0.05) were identified by using DESeq2 (v.1.22.2). |
WBPaper00061952:daf-18(nr2037)_downregulated
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Transcripts that showed significantly increased expression in BAT525 [hmg-3 (tm2539) / dpy-5(e61) unc-13(e1091) I.] comparing to in N2 at 1-day post L4 adult hermaphrodite stage. |
DESeq 2, fold change > 4, adjusted p-value < 0.05. |
WBPaper00055013:hmg-3(bar24)_upregulated
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Transcripts that showed significantly decreased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Psora-Allantoin_downregulated
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Transcripts that showed significantly decreased expression after animals were treated with 100uM Psora from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Psora_downregulated
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Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Rapamycin-Metformin_downregulated
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Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 50uM Rifampicin from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Rapamycin-Rifampicin_downregulated
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Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Rifampicin-Allantoin_downregulated
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Transcripts that showed significantly decreased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Rifampicin_downregulated
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