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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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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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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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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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Genes down regulated by mir-243(n4759). |
RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243. |
WBPaper00036130:mir-243_down_regulated
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Genes downregulated in dcr-1(-/-) adult animals by at least 1.5 fold and P < 0.01, as determined by a multisample t-test and the Benjamini and Hochberg false discovery rate correction. |
Statistical t-test: P < 0.05 for rde-4(-/-) and rde-1(-/-) analyses; P < 0.01 for dcr-1(-/-) analysis with a threshold of 1.5-fold misregulation. |
WBPaper00029437:dcr-1_downregulated
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Transcripts that showed significantly decreased expression in sek-1(km4) animals comparing to in N2 animals under both dietary (DR, OP50 OD = 0.1) and ad libtum (AL, OP50 OD = 3) conditions from 3-day post L4 till 6-day post L4 adult hermaphrodite stage. |
Bioconductor package edgeR, p < 0.05. |
WBPaper00056443:sek-1(km4)_downregulated
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Bacteria infection: Xenorhabdus nematophila |
Caenorhabditis elegans Genes with expression levels changed significantly after treatment of Xenorhabdus nematophila. |
Differential expression were calculated by empirical eBayes method using eBayes function. P_value <= 0.01 and log2 fold change > 1 were used to call differentially expressed genes in all datasets. |
WBPaper00041606:CE_X.nematophila_regulated
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Genes that showed significantly altered expression in plep-1(ttTi53821) comparing to in N2 young adult animals. |
Technical replicate correlation was estimated with the function duplicateCorrelation, and differential expression for the N2-QG2458 contrast was estimated by linear model. |
WBPaper00048657:plep-1(ttTi53821)_regulated
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Transcripts with significantly increased expression after treatment with 0.1mM paraquat vs. control |
Comparisons of each genotype were compared to the wild-type using the Empirical Base (Wright & Simon) algorithm and fold changes were represented on a log2 scale. A threshold of p < 0.05 and a fold change of 1.3 (log2) was set to determine differentially expressed targets. |
WBPaper00045263:0.1mM-paraquat_upregulated
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Transcripts that showed significantly increased expression in hsf-1(RNAi) animals comparing to in control animals, without heat shock. |
Transcripts that were differentially expressed in different conditions, compared to the hsf-1(+);-HS control, were determined with CuffDiff, which uses the Benjamini-Hochberg correction for multiple testing to obtain the q-value (the FDR-adjusted the p-value). |
WBPaper00049942:hsf-1(RNAi)_upregulated
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Genes with expression altered >= 3-fold in dpy-9(e12) 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-9_regulated
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Genes from eat-2(ad465) animals with significantly increased expression after 72 hours of treatment on growth media with 10uM rapamycin in 2% DMSO. |
Analysis of gene expression data was carried out with the Affymetrix Transcriptome Analysis Console. Data preprocessing (using RMA normalization) and QC metrics were performed using Affymetrix Expression Console TM and manually inspected afterwards. Expression analysis was carried out for each two pairwise conditions. FDR statistical correction for multiple testing resulted in a slightly lower number of DEGs in most cases. P-value < 0.05 and fold change > 2.0 were used to determine differentially expressed genes. |
WBPaper00048989:eat-2(ad465)_rapamycin_upregulated
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Transcripts that interact with 3xFLAG-DLC-1 as identified by immunoprecipitation followed by RNA sequencing. |
DESeq2, fold change > 2,, p-value < 0.01 |
WBPaper00055334:DLC-1_interacting
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Transcripts that showed significantly decreased expression after 24 hour exposure to 20umol/l Triclosan at L4 larva stage. |
Fold change > 2, p-value < 0.05. |
WBPaper00051387:Triclosan_downregulated
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mRNAs that showed significantly increased expression in polysomal fractions in daf-2(e1370) comparing to in daf-2(e1370);daf-16(mu86), according to RNAseq study. |
Differentially expressed genes were determined using cuffdiff across all pairs. |
WBPaper00046337:polysomal_daf-2_vs_daf-2;daf-16_upregulated
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Transcripts that showed significantly decreased expression in mrps-5(RNAi) comparing to in control animals. |
Fold change > 4, p-value < 0.01 |
WBPaper00056330:mrps-5(RNAi)_downregulated
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Treatment with 2.0mM of HuminFeed until young adult stage (3 days). |
Gene significantly down-regulated by treatment with 2.0mM of HuminFeed until young adult stage (3 days), with a minimum fold change in gene expression of 0.8. |
For selection of DEGs, an unpaired t -test was performed followed by a significance analysis of microarray (SAM) test including a calculation that estimates the false discovery rate (FDR). FDR, reducing on the one hand type I errors for null associations, was set to a non-stringent level of <12.5%, mainly to guard from an increase of type II error and also based on findings by Levine et al. (2011), which described 12.5% as most acceptable optimum level of FDR, representing the 90th percentile of the normal distribution curve. DEGs exceeding a fold change of 1.25 were further analyzed with respect to their functional clustering. This fold-cut-off was chosen to allow an interpretation that is biologically meaningful, akin to the notion that data of sound technical and experimental quality which returns strong, statistically significant, absolute signal intensities is sufficiently robust to justify a fold-cut-off of >1.2. This analysis was conducted using the functional annotation clustering tool of the Database for Annotation, Visualization, and Integrated Discovery (DAVID; Huang et al., 2007). |
WBPaper00041002:HF_3d_2.0mM_Down
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FBF-associated probe sets (FDR <2.25%) |
SAM assigns a score to each probe set and estimates their false discovery rates (FDRs). SAM deemed 4722 probe sets as significantly enriched at an FDR of 2.25% or lower. |
WBPaper00035905:FBF-1_Associated
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heat shock: 33C 30min |
Transcripts that showed significantly increased expression in hsf-1(RNAi) animals, after heat shock at 33 C for 30min, comparing to in hsf-1(RNAi) animals without heat shock. |
Transcripts that were differentially expressed in different conditions, compared to the hsf-1(+);-HS control, were determined with CuffDiff, which uses the Benjamini-Hochberg correction for multiple testing to obtain the q-value (the FDR-adjusted the p-value). |
WBPaper00049942:HeatShock_upregulated_hsf-1(RNAi)
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Bacteria infection: Serratia marcescens |
Caenorhabditis elegans Genes with expression levels changed significantly after treatment of Serratia marcescens. |
Differential expression were calculated by empirical eBayes method using eBayes function. P_value <= 0.01 and log2 fold change > 1 were used to call differentially expressed genes in all datasets. |
WBPaper00041606:CE_S.marcescens_regulated
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Transcripts that showed significantly decreased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. |
DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. |
WBPaper00050859:downregulated_P-granule(-)GFP(+)_vs_control_day2-adult
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Genes that were enriched in oogenic fog-2(q71) gonads comparing to in spermatogenic fem-3(q96gf), according to RNAseq analysis. |
To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. |
WBPaper00045521:Oogenic
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948 reproductively enriched mRNAs that co-immunoprecipitate with GLD-1. To identify GLD-1 mRNA targets, authors performed immunoprecipitation (IP) of GLD-1, followed by microarray analysis of the co-IPed mRNAs (RIP-chip). Extracts from young adult transgenic worms expressing a rescuing FLAG and GFP-tagged GLD-1, hereafter referred to as tagged GLD-1, were subjected to IP in triplicate with anti-FLAG (aFLAG IP) or anti-MYC (aMYC IP) antibodies as controls. Comparison of aFLAG IP versus aMYC IP to input revealed a large population of GLD-1-associated transcripts. Authors additionally performed complementary aFLAG IPs upon worms expressing either tagged GLD-1(GGF IP) or non-tagged GLD-1(N2 IP). Comparing transcript 'IP-enrichment values' from both approaches revealed a correlation of 0.96, which indicated high reproducibility of GLD-1 association with specific mRNAs even on a quantitative level. |
Authors calculated the mean IP enrichment from the two analyses and given a cutoff of three-fold, they identified 948 reproducibly enriched mRNAs (14.2%) from of a total of 6635 detected by the array. |
WBPaper00037901:GLD-1_mRNA_targets
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Oxidative stress. |
Genes downregulated by oxidative stress. |
Assessed by SAM (Significance Analysis of Microarray) [false discovery rate (FDR) = 11%] |
WBPaper00034757:down_by_oxidative_stress
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Treatment with 2.0mM of HuminFeed until older adult stage (11 days). |
Gene significantly up-regulated by treatment with 2.0mM of HuminFeed until older adult stage (11 days), with a minimum fold change in gene expression of 1.25. |
For selection of DEGs, an unpaired t -test was performed followed by a significance analysis of microarray (SAM) test including a calculation that estimates the false discovery rate (FDR). FDR, reducing on the one hand type I errors for null associations, was set to a non-stringent level of <12.5%, mainly to guard from an increase of type II error and also based on findings by Levine et al. (2011), which described 12.5% as most acceptable optimum level of FDR, representing the 90th percentile of the normal distribution curve. DEGs exceeding a fold change of 1.25 were further analyzed with respect to their functional clustering. This fold-cut-off was chosen to allow an interpretation that is biologically meaningful, akin to the notion that data of sound technical and experimental quality which returns strong, statistically significant, absolute signal intensities is sufficiently robust to justify a fold-cut-off of >1.2. This analysis was conducted using the functional annotation clustering tool of the Database for Annotation, Visualization, and Integrated Discovery (DAVID; Huang et al., 2007). |
WBPaper00041002:HF_11d_2.0mM_Up
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Transcripts that were activated by CEH-23 by comparing expression between isp-1(qm150) and ceh-23(ms23);isp-1(qm150). |
Identified by 1 class SAM with FDR=0.59, 1.5 fold gene cutoff. |
WBPaper00051304:CEH-23_activating
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