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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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Transcripts that showed significantly increased 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_upregulated
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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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Transcripts that showed significantly decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage. |
DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed. |
WBPaper00048971:daf-16(mgDf50)_downregulated_L1
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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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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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Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis. |
To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. |
WBPaper00045521:Gender_Neutral
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Genes found to be regulated by low-copy overexpression of sir-2.1 with p < 0.014. |
N.A. |
WBPaper00026929:sir-2.1_overexpression_regulated
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Germline-intrinsic transcripts. |
Comparisons were made between genotypes by subtracting the mean log value of one ratio from another, and the significance of the difference was evaluated using Student t-test for two populations. For the fem-3(gf) versus fem-1(lf) direct comparison, authors performed the same analysis, except they used a Students t-test for one population. Author chose a combination of a twofold difference with a t value exceeding 99% confidence (P < 0.01), because these criteria allowed the inclusion of essentially all genes that had previously been identified as germline-enriched in a wt/glp-4 hermaphrodite comparison. Additionally, requiring a twofold difference reduced false positives, as the number of genes with two-fold difference and a P<0.01 only included ~100 genes more than with P < 0.001, and almost all genes showed germline expression by in situ hybridization. |
[cgc6390]:intrinsic
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Transcripts that showed significantly increased expression in ints-5(RNAi) comparing to in N2. |
DESeq2 and edgeR. |
WBPaper00056284:ints-5(RNAi)_upregulated
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Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference). |
A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. |
WBPaper00037950:AVA-neuron_L1-larva_expressed
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Transcripts that showed significantly depleted expression in sensory neuron (labeled by iaIs25[Pgcy-37::GFP + unc-119(+)]) comparing to in whole worm. |
Fold change > 2, p-value < 0.05. |
WBPaper00060661:sensory-neuron_depleted
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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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Significantly downregulated genes from cyc-1(RNAi) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips. |
SAM algorithm with an FDR < 0.1. |
WBPaper00033065:cyc-1(RNAi)_downregulated
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Genes identified as down-regulated at a 5% false discovery rate through RNAseq experiments with three tatn-1(qd182) and three N2 RNA samples. |
ANOVA with FDR <= 0.05. |
WBPaper00044656:tatn-1(qd182)_downregulated
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Fungi infection: Harposporium sp. |
Genes with decreased expression after 24 hours of infection by Harposporium 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:Harposporium_24hr_downregulated_RNAseq
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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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Transcripts that did not alter expression in smg-1(r910) and smg-1(r910) smg-2(r915) mutants comparing to in N2, but their mRNAs co-purify with SMG-2. |
edgeR |
WBPaper00053308:SMG-2_associated_NMD(-)_unaltered_ClassII
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Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin, 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:Rapamycin-Rifampicin-Allantoin_upregulated
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Transcripts that showed significantly increased 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_upregulated
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Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 100uM Psora from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Rifampicin-Psora_upregulated
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Genes with decreased RNA expression after 24 hours rotenone treatment |
EdgeR provides statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed. |
WBPaper00044426:rotenone_24h_downregulated
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Transcripts that showed significantly altered expression after 24 hour exposure to zidovudine (AZT) starting at L1 lava stage. |
DESeq |
WBPaper00053302:zidovudine_72h_regulated
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Expression Pattern Group H, enriched for genes involved in embryonic development. These patterns have in common that they all have genes of which the expression goes up after the juvenile stage. The expression of the genes in these patterns remains high or even goes up after reproduction. |
The significance (P 0.0001) of the relative age (time) was used to determine if a gene was differentially expressed between the three age (time) groups. The effect of this factor explaining gene expression differences was used to determine if the expression went up or down during the two age/time periods (t1 - t2 and t2 -t3). Authors used a permutation approach to determine the thresholds for the different mapping strategies. For each of the used models for eQTL mapping, authors used 23,000 permutations. For each permutation, authors randomly picked a spot; each spot could only be picked once. The gene expression and relative lifespan values were than randomly distributed over the RILs (and time points) and used for mapping. In this way, authors obtained a threshold for each of the explaining factors. For the single time points, authors used a FDR of 0.01 to adjust for multiple testing. The genome-wide threshold for this FDR is -log10 P = 3.8 for each of the three time points. For the combined models (t1 to t2 and t2 to t3), authors used a genome-wide threshold of -log10 P = 4, which resembles an FDR of 0.006, 0.001, and 0.006 for marker, age, and the interaction between marker and age, respectively. To determine the threshold for the single gene examples, authors used 1000 permutations as in the genome-wide threshold. The difference is that they use the gene under study in all of the permutations. The P-values for the gene specific thresholds were determined at FDR = 0.05. |
WBPaper00036286:Pattern_H
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Genes that exhibit a differential enrichment (p-value < 0.05 and a fold enrichment (log2fold)> 0.5) between the ADR-2 IPs from N2 and adr-2(ok735)worms. |
DESeq2, p-value < 0.05 and a fold enrichment log2fold > 0.5. |
WBPaper00055226:ADR-2_target_N2
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Transcripts of noncoding 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_noncoding-RNA
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Transcripts that showed significantly increased expression in ints-1(RNAi) comparing to in N2. |
DESeq2 and edgeR. |
WBPaper00056284:ints-1(RNAi)_upregulated
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Genes with expression enriched in PVD and OLL neurons. Data sets were normalized by RMA and transcripts showing relative PVD enrichment (>= 1.5X) vs. the reference sample were identified by SAM analysis (False Discovery Rate, FDR < 1%). |
Data sets were normalized by RMA and transcripts showing relative PVD enrichment (>=1.5X) vs. the reference sample were identified by SAM analysis (False Discovery Rate, FDR < 1%) |
WBPaper00036375:enriched_in_PVD_OLL
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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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Genes that are enriched in male Z1 and Z4 daughter cells according to RNAseq analysis towards FACS sorted Z1 and Z4 daughter cells. |
Cuffdiff v2.1.1 |
WBPaper00048690:male-Z1-Z4-daughter_enriched
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