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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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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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Genes with significantly increased expression in eat-2(ad465) treated with 2% DMSO for 72 hours, comparing to in N2 treated with 2% DMSO for 72 hours. |
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)_upregulated_in-DMSO
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Genes expressed in N2. |
Expressed transcripts were identified on the basis of a Present call in 3 out of 4 N2 experiments as determined by Affymetrix MAS 5.0. |
WBPaper00025141:N2_Expressed_Genes
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Genes upregulated 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_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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Genes depleted in muscle cells (24hr muscle dataset). Dissociated myo-3::GFP embryos were cultured for 24 hours before FACS sorting. |
A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets. |
WBPaper00031003:24hr_muscle_depleted
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Total muscle depleted genes (complete list of non-overlapping genes from the 0hr and 24hr muscle depleted datasets). |
A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets. |
WBPaper00031003:total_muscle_depleted
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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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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 third UVC dose (48h). |
Genes differentially expressed under EtBr treatment and UVC exposure vs under UVC exposure but without EtBr treatment at the -1h timepoint (just prior to the third UVC dose (48h)). |
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_48h
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Genes that showed lower 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:N2lessDR1350
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Genes from N2 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:N2_rapamycin_upregulated
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Genes expressed in embryonic motor neurons (identified by unc-4::GFP expressing cells). |
Genes called Present by MAS 5.0 in 2 out of 3 unc-4::GFP hybridizations. |
WBPaper00025141:unc-4::GFP_Expressed_Genes
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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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Embryonic Pan-neural Enriched Genes. |
A two-class unpaired analysis of the data was performed to identify genes that differ by >= 1.5-fold from the reference at a FDR of <1% for the larval pan-neural, embryonic pan-neural, and larval A-class motor neuron datasets. |
WBPaper00030839:Embryo_Pan_Neuronal
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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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Genes from eat-2(ad465) animals with significantly decreased 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_downregulated
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Genes downregulated (fold changes < 2-fold) in the worms following exposure of a-SWCNTs (500 mg\/mL) for 48 hr. |
N.A. |
WBPaper00042331:a-SWCNTs_downregulated
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Transcripts that showed significantly increased expression in N2 animals exposed to fluvastatin sodium for 9 hours at L4 larva stage, comparing to N2 animals grown without fluvastatin exposure. |
DESeq2 FDR < 0.05 |
WBPaper00059604:fluvastatin_upregulated_N2
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Transcripts that showed significantly decreased expression in daf-2(e1370) comparing to in N2. |
Student's t-test, fold change > 2, p-value < 0.05. |
WBPaper00055386:daf-2(e1370)_downregulated
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Genes that showed significantly decreased expression in daf-19(m86);daf-12(sa204) comparing to in daf-12(sa204), at 2-day post-L4 adult hermaphrodite stage. |
BRB Array Tools were used to identify genes with statistically significant variation in expression. The probability threshold was set at a maximum of 0.05 (p-value <= 0.05) for genes to be considered statistically differentially expressed in wild-type and mutant populations. Genes with a signal variation of 1.5-fold or greater were selected for subsequent experiments. To reduce false discoveries, a class comparison test was conducted using a multivariate per mutation test with a confidence level of 97% (L1 analysis) and 90% (adults). |
WBPaper00053550:daf-19(m86)_downregulated_AdultDay2
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Genes that showed increased expression in xpa-1(ok698) comparing with N2 in mixed stages. |
After pre-processing and normalization, the Student t-test was executed to reveal transcripts statistically significantly regulated at the 95% confidence level (P < 0.05) between xpa-1 and WT. |
WBPaper00042234:xpa-1_upregulated
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Genes depleted in muscle cells (0hr muscle dataset). Dissociated myo-3::GFP embryos were cultured for 0 hours before FACS sorting. |
A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets. |
WBPaper00031003:0hr_muscle_depleted
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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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Light/Dark cycle |
Transcripts that cycle both in LD (light/dark) and DD (constant darkness) (pF24<0.02). |
ANOVA prescreening and Fourier analysis. |
WBPaper00037695:LD_DD_6-day
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Genes that are significantly down regulated in tdp-1(ok803) poly(A) RNA-seq verses in N2. |
DESeq v1.14, with cut-off p-value < 0.05 and FDR < 0.1. |
WBPaper00046012:tdp-1(ok803)_downregulated
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Light/Dark cycle |
Transcripts that cycle in LD(light/dark) but not in DD(constant darkness) (pF24<0.02) |
ANOVA prescreening and Fourier analysis. |
WBPaper00037695:LD_3-day
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Genes with decreased expression in gei-8(ok1671) homozygous mutants comparing with N2. |
Microarray chip data was analyzed by Affymetrix MAS 5.0 suite software (1.6-fold change in mRNA expression) and Robust Multichip Average (RMA) (1.2-fold change in mRNA expression) as part of the Partek genomics suite software package, all with a p-value less than or equal to 0.05 |
WBPaper00042128:gei-8(ok1671)_downregulated
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Genes with significantly decreased expression in lin-35(n745) comparing to in N2 in starvation condition. |
Statistical t-test: P < 0.015 for lin-35(n745) analysis with a threshold of 2-fold ratio of mis-regulation. |
WBPaper00048637:lin-35(n745)_starvation_downregulated
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Protein coding genes with decreased expression in prg-1(wm161) comparing to in N2. |
Cuffdiff and DEGseq were used to calculate the differential expression of protein-coding genes with and without the prg-1 mutation, and authors selected genes which had more than two-fold difference in expression (P < 0.05, q < 0.01 of Storey) from DEGseq outcomes. The intersection of genes which authors selected from DEGseq outcomes and genes which had more than two-fold difference in expression (P < 0.05) from Cuffdiff outcomes was defined as differentially expressed genes. |
WBPaper00045316:prg-1_downregulated_L2
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