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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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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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Genes with expression level regulated by genotype (N2 vs CB4856) 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_regulated_developing
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Transcripts that showed significantly increased expression in npr-15(tm12539) comparing to in N2 at L4 larva stage. |
Fold change > 2, FDR < 0.05. |
WBPaper00066608:npr-15(tm12539)_upregulated
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Transcripts that showed significantly decreased expression after exposure of to 10 mg per liter of SiNPs for 24 h. |
Fold change and Welcht-test performed between probes per gene and were applied to selectdifferentially expressed genes (DEGs): the fold change threshold was 2-fold and the significance level was p < 0.05. |
WBPaper00057098:SiO2-nanoparticles_downregulated
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Genome-wide analysis of developmental and sex-regulated gene expression profile. |
self-organizing map |
cgc4489_group_11
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Treatment with 0.2mM of HuminFeed until young adult stage (3 days). |
Gene significantly up-regulated by treatment with 0.2mM of HuminFeed until young adult stage (3 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_3d_0.2mM_Up
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Bacteria diet: Lactobacillus rhamnosus CNCM I-3690 |
Differentially expressed genes between C.elegans fed with L.rhamnosus strain CNCM I-3690 and control strain E.coli OP50 after 3 days of feeding. |
Differential expression was assayed via limma. Genes were considered differentially expressed when the multiple testing adjusted P-value < 0.01. |
WBPaper00041906:I-3690_vs_OP50_3d
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Genes that showed significant differential expressed between control and 150 mg\/L Atrazine treatment. |
t-test, p < 0.05. |
WBPaper00036123:Atrazine_regulated
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Differentially-expressed genes in the MA lines. |
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WBPaper00025099:MA_specific
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Genes found to be regulated in daf-16(mgDf50) by resveratrol treatment with p < 0.01. |
N.A. |
WBPaper00026929:Resveratrol_regulated_daf-16
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Genes down regulated in the absence of TDP-1, when the threshold was set at a fold change (FC) of 1.2. |
The management and statistical analysis of the microarray data were performed using the Partek Genomic Suite (Partek, Missouri) and Spotfire DecisionSite software (TIBCO, California). |
WBPaper00040603:tdp-1(lf)_down_vs_N2_FC_1.2
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Genes with expression level regulated by genotype (N2 vs CB4856) at Old adults stage (214 hours at 24 centigrade). |
Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0136. |
WBPaper00040858:eQTL_regulated_old
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Genes enriched in intestine. |
To identify genes that are significantly enriched by mRNA tagging, we first normalized the total amount of Cy3 and Cy5 signal to each other in each hybridization. We measured the ratio of the signals from the co-immunoprecipitated mRNA (Cy5) to total RNA in the cell extract (Cy3), and calculated the percentile rank for each gene relative to all genes in each hybridization. The mean percentile rank was determined from eight repeats of the mRNA-tagging experiment. Student's t-test was used to determine which genes showed a mean enrichment significantly greater than the median enrichment for all genes (P<0.001). |
WBPaper00026980:intestine_enriched
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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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Transcripts that showed significantly decreased expression in ash-2(RNAi) comparing to in wild type animals injected with vector. |
Differential mRNA expression using DESeq2. mRNAs with a FDR < 0.05 and fold change > 2 considered differentially expressed. |
WBPaper00066232:ash-2(RNAi)_downregulated_WT
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Genes with more than 2 fold increase of expression after 500 mg/l acrylamide treatment comparing with control. |
Two-sided t-test, p < 0.005. |
WBPaper00031184:acrylamide_upregulated
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Transcripts that showed significantly decreased expression in unc-30(ok613) animals at L4 larva stage, comparing to N2 animals. |
Genes exhibiting at least two-fold change were considered differentially expressed. |
WBPaper00061439:unc-30(ok613)_downregulated
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Transcripts with significantly decreased 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_downregulated
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Transcripts with significantly decreased expression in isp-1(qm150) vs. N2, and in isp-1(qm150)ced-4(n1162) vs. ced-4(n1162). |
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:isp-1(qm150)_downregulated
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Transcripts with significantly decreased expression in nuo-6(qm200) vs. N2, and in nuo-6(qm200);ced-4(n1162) vs. ced-4(n1162). |
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:nuo-6(qm200)_downregulated
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Transcripts with significantly decreased expression under all of these conditions |
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:ProLongevity-mtROS_downregulated
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Expression Pattern Group E, enriched for genes involved in dephosphorylation. |
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_E
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spermatogenesis-enriched |
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]:spermatogenesis-enriched
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Transcripts that showed significantly decreased expression in animals exposed to 400uM tamoxifen from L1 to L4 larva stage. |
DEseq2, fold change > 2 |
WBPaper00064505:tamoxifen_downregulated
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Bacteria diet: Comamonas sp. DA1877 |
Genes upregulated on Comamonas DA1877 relative to E. coli OP50, Gravid adult stage |
Moderated T statistics in Limma was used to calculate significance. Significance was determined using an adjusted p value. Changes in gene expression that were 2-fold (p < 0.001) or greater were considered significantly changed. |
WBPaper00042258:DA1877_upregulated_GravidAdult
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Differentially expressed genes during worm lifespan. Medoid 2 Fig.4. |
Hierarchical clustering |
WBPaper00032165:differentially_expressed_with_age_medoid_2
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Genes up-regulated after 100 um Quercetin treatment. Fold change > 1.25. |
GCRMA |
WBPaper00040963:Q100_up
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Genes up-regulated after 200 um Quercetin treatment. Fold change > 1.25. |
GCRMA |
WBPaper00040963:Q200_up
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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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