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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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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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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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Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. |
N.A. |
WBPaper00064071:NHR-49_interacting
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Transcripts that showed altered expression in cat-1(RNAi) animals comparing to control animals injected with empty vector. |
p-value <= 0.05 |
WBPaper00066902:cat-1(RNAi)_regulated
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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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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 expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging. |
Cufflinks FPKM value >=1. |
WBPaper00050990:NMDA-neuron_expressed
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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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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 rrf-3(pk1426) comparing to in N2 at embryo stage. |
DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. |
WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
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Bacteria infection: Bacillus thuringiensis |
mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq. |
Cuffdiff, ajusted p-value < 0.01. |
WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
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Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2. |
DESeq2, fold change > 2, p-value < 0.01. |
WBPaper00061203:sin-3(tm1276)_upregulated
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Bacteria infection: Bacillus thuringiensis |
mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq. |
Cuffdiff, ajusted p-value < 0.01. |
WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
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Transcripts detected in germline isolated from day-1 adult hermaphrodite animals. |
All three experiments have CPM >= 1. |
WBPaper00067147:germline_expressed
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Proteins interacting with GST-FBXA-210(C-terminal) via IP-MS in young adult animals. Proteins shown here are enriched in GST |
Fold change > 2 and p-value < 0.1 were defined as threshold for significance. |
WBPaper00068277:FBXA-210(C-terminal)_interacting_YoungAdult
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Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2. |
DESeq2, Fold change > 1.5. |
WBPaper00051404:alg-1(gk214)_upregulated
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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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Significantly upregulated genes from clk-1(qm30) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips. |
SAM algorithm with an FDR < 0.1. |
WBPaper00033065:clk-1(qm30)_upregulated
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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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Bacteria infection: Staphylococcus aureus |
Transcripts that showed significantly decreased expression in animals experimentally colonised by a wild microbiota community and infected by the widespread animal pathogen, Staphylococcus aureus, comparing to animals not colonized by microbiota and not infected by pathogen. |
DeSeq2 (v. 1.42.0), Wald analyses testing against a null hypothesis of < |1.5|-fold change in gene expression between treatments (BenjaminiHochberg adjusted false detection rate of p <= 0.05. |
WBPaper00067479:Microbiota-Pathogen_vs_control_downregulated
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Bacteria infection: Staphylococcus aureus |
Transcripts that showed significantly decreased expression in animals experimentally colonised by a wild microbiota community and infected by the widespread animal pathogen, Staphylococcus aureus, comparing to animals colonized by microbiota but not infected by pathogen. |
DeSeq2 (v. 1.42.0), Wald analyses testing against a null hypothesis of < |1.5|-fold change in gene expression between treatments (BenjaminiHochberg adjusted false detection rate of p <= 0.05. |
WBPaper00067479:Microbiota-Pathogen_vs_Microbiota_downregulated
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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 decreased expression in N2 day 7 adults comparing to in N2 day 1 adult animals according to Oxford Nanopore Technologies Direct RNA sequencing (Nanopore DRS). |
DESeq fold change > 2, FDR < 0.05. |
WBPaper00067499:Day7_vs_Day1_downregulated_Nanopore
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Transcripts that showed significantly decreased expression in N2 day 10 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. |
DESeq fold change > 2, FDR < 0.05. |
WBPaper00067499:Day10_vs_Day1_downregulated_Illumina
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Transcripts that showed significantly decreased expression in N2 day 15 adults comparing to in N2 day 1 adult animals according to Illumina RNASeq. |
DESeq fold change > 2, FDR < 0.05. |
WBPaper00067499:Day15_vs_Day1_downregulated_Illumina
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Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. |
DESeq2, fold change > 2, adjusted p-value < 0.01 |
WBPaper00058598:sin-3(tm1276)_downregulated
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Transcripts depleted in purified oocyte P bodies comparing to in whole oocytes. |
DESeq2, FDR < 0.05, fold change > 2. |
WBPaper00065975:P-body_vs_oocyte_depleted
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