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Genes with expression altered >= 3-fold in dpy-10(e128) mutants. |
Data across the wild type series was analyzed using the Significance analysis of Microarrays (SAM) algorithm (to calculate the False Discovery Rate (FDR)). |
WBPaper00035873:dpy-10_regulated
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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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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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Genes that were upregulated in lin-15B(n744). |
For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis. |
WBPaper00038168:lin-15B(n744)_upregulated
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Bacteria infection: Enterococcus faecalis |
Genes with increased expression after 24 hours of infection by E.faecalis 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:E.faecalis_24hr_upregulated_TilingArray
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Fungi infection: Myzocytiopsis humicola |
Transcripts that showed significantly altered expression 12 hours after animals were infected by M. humicola. |
Differentially expressed genes as determined by Kallisto and Sleuth (pval<0.01, qval<0.1). |
WBPaper00060871:M.humicola-infection_12h_regulated
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Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. |
N.A. |
WBPaper00064071:NHR-49_interacting
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Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards total RNA. |
Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference. |
WBPaper00045974:NSM_enriched_totalRNA_RNAseq
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Genes that are significantly up regulated in tdp-1(ok803) poly(A) RNA-seq verses in N2. |
DESeq v1.14, with cut-off p-value < 0.05 and FDR < 0.1. |
WBPaper00046012:tdp-1(ok803)_upregulated
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Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging. |
Cufflinks FPKM value >=1. |
WBPaper00050990:hypodermis_expressed
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Genes up regulated in alg-1(gk214) comparing to in N2. |
Differential expression was assessed using an empirical Bayes statistics using the eBayes function. |
WBPaper00040823:alg-1(gk214)_upregulated
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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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Maternal class (M): genes that are called present in at least one of the three PC6 replicates. |
A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. |
[cgc5767]:expression_class_M
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Transcripts that showed significantly increased expression in mrg-1(qa6200) comparing to in control animals in primordial germ cells (PGCs) at L1 larva stage. |
DESeq2(v1.32.0), FDR < 0.05. |
WBPaper00064315:mrg-1(qa6200)_upregulated_PGCs
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Strictly maternal class (SM): genes that are the subset of maternal genes that are not also classified as embryonic. |
A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. |
[cgc5767]:expression_class_SM
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Transcripts that showed significantly increased expression in nhr-114(gk849) comparing to wild type animals at L4 larva. |
DESeq2 1.26.0, fold change > 2, FDR < 0.05. |
WBPaper00064539:nhr-114(gk849)_upregulated
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Transcripts that showed significantly increased expression at the intestine cells of daf-2(e1370) comparing to the intestine cells of N2 animals at L2 larva stage. |
DESeq2 (version 1.24.0), fold change >= 2, FDR < 0.05 |
WBPaper00064632:daf-2(e1370)_upregulated_intestine
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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 increased expression in daf-2(e1370) comparing to in control animals. |
NOIseq(v2.34.0), fold change > = 1.5, Differentially expressed genes (DEGs) were defined as having a probability of differentialexpression > 95%. |
WBPaper00064727:daf-2(e1370)_upregulated
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Significantly differentially expressed genes as determined by microarray analysis of wild-type and cde-1 mutant germlines. |
RNAs that changed at least 2-fold with a probability of p < 0.05 were considered differentially regulated between wildtype and cde-1. |
WBPaper00035269:cde-1_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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Transcripts that showed significantly increased expression in wdr-5(ok1417);skn-1(lax188) comparing to in skn-1(lax188) at day 2 adult stage. |
fold change > 2 |
WBPaper00058711:wdr-5(ok1417)_upregulated
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Starvation |
Starvation-induced transcripts that showed significantly increased expression in post dauer animals comparing to wild type control. |
edgeR |
WBPaper00053713:Starvation-induced_postdauer_vs_control_upregulated
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Proteins that showed significantly decreased expression in 1-day-old sek-1(km4) adults comparing to in wild type animals, both with 6 hours of cisplatin treatment. |
The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data. |
WBPaper00065373:sek-1(km4)_downregulated_cisplatin
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Transcripts that showed significantly decreased expression in strain GC1459 containing daf-18(ok480) comparing to control strain GC1171. |
edgeR, p-value < 0.05, fold change > 2. |
WBPaper00061699:daf-18(ok480)_downregulated
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Genes that showed oscillating mRNA expression level throughout the 16 hour time courses from L3 larva to young adult. |
The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak. |
WBPaper00044736:oscillating_dev_expression
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Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in N2. |
Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1. |
WBPaper00053810:daf-2(e1370)_upregulated
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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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