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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 that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
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Genes upregulated in rde-4(-/-) adult animals by at least 1.5 fold and P < 0.05, as determined by a multisample t-test. |
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:rde-4_upregulated
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WT-Pico Pan-neural Depleted Genes, with genes found multiple times in a single dataset removed (without dups). |
To identify differentially expressed transcripts, normalized intensity values from the pan-neural data sets were compared to a reference (from all larval cells) using Significance Analysis of Microarray software (SAM). A two class unpaired analysis of the data was performed to identify neuron-enriched genes. Pan-neural enriched transcripts in the IVT and WT-Pico-derived data set were defined as 1.5X elevated vs the reference at a False Discovery Rate (FDR) = 3%. |
WBPaper00031532:Larva_Pan_Neuronal_Depleted
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Exposure to Au-NP. |
Genes with differeiential expression after exposed to Au-NP. |
Hierarchical clustering was performed in Partek to confirm that the samples match to the treatment groups. Analysis of variance (ANOVA) was used to partition the variance due to treatment from technical and biological noise. The list of differentially expressed genes was generated by identifying the genes showing fold change of more than 1.5 and less than -1.5 at p < 0.05 with and without multiple sample correction, False Discovery Rate (FDR). False discovery correction according to Benjamini and Hochberg produced a list of 37 significant transcripts. FDR was not applied when selecting differential expressed genes, because this approach can increase the type II error and result in elimination of the genes responsive to the treatment. |
WBPaper00040821:Au-NP_regulated
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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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Treatment with 2.0mM of HuminFeed until young adult stage (3 days). |
Gene significantly up-regulated by treatment with 2.0mM 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_2.0mM_Up
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EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at just prior to the second UVC dose (24h). |
Genes differentially expressed under EtBr treatment without UVC exposure vs after UVC exposure but without EtBr treatment at the -25h timepoint (just prior to the second UVC dose (24h)). |
Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. |
WBPaper00041939:EtBr-exposed_vs_UVC-exposed_24h
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UVC-EtBr-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total) and exposed to EtBr (5ug/mL in agar).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at just prior to the second UVC dose (24h). |
Genes differentially expressed under EtBr treatment and UVC exposure vs under UVC exposure but without EtBr treatment at the -25h timepoint (just prior to the second UVC dose (24h)). |
Transcripts were defined as fold-change >1.2, p < 0.05 based on Rosetta Resolver analysis for all pairwise treatment comparisons. The fold-change refers to the second intensity over the first. |
WBPaper00041939:UVC-EtBr-exposed_vs_UVC-exposed_24h
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Exposed to males for 8 days. |
Genes down regulated in hermaphrodites after 8 days of exposure to males. |
To identify significantly regulated genes between the -male and +male conditions, authors used the Rank Products methods (R package RankProd), using the batch information to adujst for experiment specific biases, and set a False Discovery Rate (FDR) threshold for discovery of genes of 5%. From this analysis, 341 probes on the array were significantly up-regulated in the male treated samples, and 289 were significantly down-regulated. |
WBPaper00044535:male_downregulated
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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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Starvation 2-4 hours at L1 larva stage since hatching. |
Genes that showed significantly changed expression by starvation for 2-4 hours after hatch, by comparing N2 starved and N2 fed animals at L1 larva. |
Normalized log2 GCRMA values were used to assess significance of expression changes with the LIMMA/GCRMA empirical Bayes test. A threshold for significance at a q-value (FDR) of less than 0.05 was used to determine if a gene is differentially expressed. |
WBPaper00053236:Starvation_regulated_N2
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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 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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Bacteria Diet: L. plantarum with pdxH mutant vs. L. plantarum |
Transcripts that showed significantly decreased expression in N2 animals fed with L. plantarum with pdxH mutant, comparing to in N2 animals fed with L. plantarum. |
GFold3, logFC < -1 or > 1. |
WBPaper00066703:L.plantarum-pdxH_downregulated
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Warm/Cold cycle |
Transcripts that cycle in warm/cold (WC) condition but not in constant cold (CC) condition (pF24<0.02). |
ANOVA prescreening and Fourier analysis. |
WBPaper00037695:WC_5-day
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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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Genes with a >= 10-fold decrease in expression in Day 15 adults relative to expression levels in Day 6 adults are listed. |
To determine age-dependent changes in gene expression the mean log ratio of gene expression at two different points during aging was calculated, and a 2-tailed unpaired Student t test was used to identify genes with statistically significant (p-value <= 0.05) changes in expression levels as a function of age. |
WBPaper00038462:aging_downregulated
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Genes that showed higher expression in N2 than in DR1350. |
The normalised data were analysed using a two-way ANOVA, testing for each gene the effects of LINE (N2, DR1350, RIL-14, RIL-17), TREATMENT (non-dauer vs dauer larva-inducing) and the LINE TREATMENT interaction, using a published PERL script. |
WBPaper00034739:N2moreDR1350
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Treatment with 0.2mM of HuminFeed Hydroquinone until young adult stage (3 days). |
Gene significantly up-regulated by treatment with 0.2mM of HuminFeed Hydroquinone 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:HQ_3d_0.2mM_Up
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Treatment with 2.0mM of HuminFeed Hydroquinone until young adult stage (3 days). |
Gene significantly up-regulated by treatment with 2.0mM of HuminFeed Hydroquinone 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:HQ_3d_2.0mM_Up
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Genes up regulated in tax-6(ok2065) comparing to in N2. |
To identify genes that were significantly differentially expressed between each mutant and the control, linear modelling and empirical Bayes analysis was performed using the limma package. Limma computes an empirical Bayes adjustment for the t-test (moderated t-statistic), which is more robust than the standard two-sample t-test comparisons. To correct for multiple testing, Benjamin and Hochbergs method to control for false discovery rate was used. Genes with an adjusted P value of 0.05 or smaller and a fold-change in expression larger than twofold were considered differentially expressed. |
WBPaper00038172:tax-6null_up_regulated
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Genes up 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)_up_vs_N2_FC_1.2
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Bacteria infection: Pseudomonas aeruginosa PA14 |
Genes upregulated in worms grown on P. aeruginosa PA14 as compared to worms grown on OP50 for 4 hours by at least 2 fold and P < 0.01, as determined by a t-test. |
At least 2 fold and P < 0.01, as determined by a t-test. |
WBPaper00028789:PA14_vs_OP50_upregulated_4hr
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Bacteria infection: Pseudomonas aeruginosa PA14 |
Genes upregulated in worms grown on wild-type P. aeruginosa PA14 as compared to worms grown on an isogenic PA14 mutant gacA for 4 hours by at least 2 fold and P < 0.01, as determined by a t-test. |
At least 2 fold and P < 0.01, as determined by a t-test. |
WBPaper00028789:PA14_vs_gacA_upregulated_4hr
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Bacteria infection: Pseudomonas aeruginosa PA14 |
Genes upregulated in worms grown on P. aeruginosa PA14 as compared to worms grown on OP50 for 8 hours by at least 2 fold and P < 0.01, as determined by a t-test. |
At least 2 fold and P < 0.01, as determined by a t-test. |
WBPaper00028789:PA14_vs_OP50_upregulated_8hr
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Bacteria infection: Pseudomonas aeruginosa PA14 |
Genes upregulated in worms grown on wild-type P. aeruginosa PA14 as compared to worms grown on an isogenic PA14 mutant gacA for 8 hours by at least 2 fold and P < 0.01, as determined by a t-test. |
At least 2 fold and P < 0.01, as determined by a t-test. |
WBPaper00028789:PA14_vs_gacA_upregulated_8hr
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Bacteria infection: Enterococcus faecalis MMH594 |
Transcripts that showed significantly increased expression after exposure to live Enterococcus faecalis MMH594 by comparing infected young adult animals with animals treated with heat-killed E.coli OP50. |
Fold-change cutoff of 2-fold (relative to heat-killed E. coli) and a Benjamini-Hochberg adjusted p-value of 0.05. |
WBPaper00053688:E.faecalis_upregulated
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Bacteria infection: Enterococcus faecium E007 |
Transcripts that showed significantly increased expression after exposure to live Enterococcus faecium E007, by comparing infected young adult animals with animals treated with heat-killed E.coli OP50. |
Fold-change cutoff of 2-fold (relative to heat-killed E. coli) and a Benjamini-Hochberg adjusted p-value of 0.05. |
WBPaper00053688:E.faecium_upregulated
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Transcripts that showed significantly increased expression after synchronized L1 larva stage animals were exposed to bare Au NPs (gold nanoparticles) for 72 hours. |
Student's t-tests, fold change > 2, p-value < 0.05. |
WBPaper00055435:AuNPs_upregulated
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