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Transcripts that showed significantly decreased expression at 11-days-post L4 adult N2 hermaphrodites comparing to 1-day-post L4 adult N2 hermaphrodites. |
DESeq2, fold change > 2, FDR < 0.05 |
WBPaper00065835:Day11_vs_Day1_downregulated
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Genes down-regulated following nhr-25(RNAi). |
Pair-wise significance testing (mutant/RNAi vs. wild-type/vector) was performed using the Bioconductor package limma and p-values were initially corrected for multiple testing using the false discovery rate (FDR) method of Benjamini and Hochberg. Authors defined differential expression as log2(ratio) >= 0.848 with the FDR set to 5%, and p-value <= 0.001. |
WBPaper00045015:nhr-25(RNAi)_downregulated
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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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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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Germline-enriched and sex-biased expression profile cluster A. |
hierarchical clustering |
[cgc6390]:Cluster_A
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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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control(maintained under normal lab light (mostly dark, in incubators).) vs 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).) at just prior to the second UVC dose (24h). |
Genes differentially expressed in control vs after UVC exposure and 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:control_vs_UVC-EtBr-exposed_24h
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control(maintained under normal lab light (mostly dark, in incubators).) vs 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).) at 3 h after the third UVC dose (51h), which is also 3 h after being placed on food. |
Genes differentially expressed in control vs after UVC exposure and EtBr treatment at the 3h timepoint (3 h after the third UVC dose (51h), which is also 3 h after being placed on food). |
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:control_vs_UVC-EtBr-exposed_51h
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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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Transcripts that showed significantly increased 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)_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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Transcripts that showed significantly increased expression in unc-30(ok613) animals at L4 larva stage after 4 hours of Pseudomonas aeruginosa infection, comparing to infected N2 animals. |
Genes exhibiting at least two-fold change were considered differentially expressed. |
WBPaper00061439:unc-30(ok613)_upregulated_P.aeruginosa-infection
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Genes up regulated in crh-1(nn3315) 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:crh-1null_up_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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Bacteria infection: Serratia marcesens |
Genes up-regulated in animals infected with Serratia marcesens compared to the E. coli OP50 control after 24h of infection. |
MAANOVA and BRB-Array-Tools. |
WBPaper00030985:Serratia_marcesens_upregulated
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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 third UVC dose (48h). |
Genes differentially expressed under EtBr treatment without UVC exposure vs after 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:EtBr-exposed_vs_UVC-exposed_48h
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mRNAs that were significantly enriched in the AIN-1 immunoprecipitation samples, compared to the control total mRNAs in the input extracts (p < 0.01). |
Signals from replicates of total worm lysates from wt and strains containing the ain-2::gfp or the ain-2 promoter::gfp transgene were mean normalized and averaged respectively to generate standard profiles of gene expression in these worm strains. Authors then calculated the ratio of signal of each gene from each IP sample to the standard gene expression profile of the corresponding worm strain. Based on this ratio, a percentile rank of each gene relative to all genes in each IP replicate was calculated. The percentile ranks in the three replicates of each IP were averaged. Student t test was utilized to determine if the average percentile ranks of enrichment of individual genes were significantly higher (p value) than the mean enrichment of all genes in the IP samples. To determine the AIN-1 or AIN-2 associated genes, we used the following criteria: (1) average percentile ranks of enrichment is greater than the mean enrichment of all genes in AIN-1 or AIN-2 IP with p < 0.01; (2) average signal in AIN-1 or AIN-2 IP replicates is greater than the background signal (including 2X standard deviation (SD)) (Background signal and SD were calculated based on signals from empty spots on each microarray); (3) criteria 1 is not be satisfied for the same gene in the corresponding control IP. |
WBPaper00031252:AIN-1_IP_enriched
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Expression Pattern Group I, enriched for genes involved in transport. |
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_I
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miRNA targets that are significantly enriched at L1 larva stage. To generate a global view of the dynamics of miRNA-mediated regulation of gene expression during C. elegans development, authors analyzed the mRNAs in the AIN-2-GFP IP results from five developmental stages. The magnitude of the combined interaction of miRNAs with a given target mRNA was assessed by measuring the fold enrichment of that mRNA in AIN-2 IP samples, relative to the abundance of the mRNA in the corresponding total lysate. Because this enrichment in the IP sample versus total lysate directly reflects the miRISC-associated fraction of a given mRNA, high enrichment indicates the likelihood of strong miRNA-mediated regulation of the mRNA, whereas low or negative enrichment indicates the likelihood of weak or absent miRNA regulation of the mRNA. It is also possible that poor enrichment could reflect interactions that occur only in a rare subset of cells at any given stage of development. Transcripts that were significantly enriched (0
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For each transcript represented on the microarray, authors first used all 18 data points from all of the 18 microarrays to calculate its average in-stage standard deviation as SD=SQRT((i=1-K (ni-1)SDi2)/(N-K)), degree of freedom (df)=N-K, where K is the number of developmental stages in which the given transcript had at least one non-missing log2(IP/Total) value; ni is the number of non-missing values in stage i among the K stages; SDi is the standard deviation of the log2(IP/Total) values from all the replicates of stage i; N is the total number of non-missing values for this transcript at all stages. A transcript must have at least one stage with at least two non-missing values to be testable. All of the non-missing values of a transcript at each stage were averaged to generate the stage-average values (Mi for stage i). The standard error of Mi was calculated as SEi=SD/SQRT(ni) (df=N-K), where SD is the average in-stage standard deviation calculated above and ni is the number of non-missing values at stage i, as explained above. Based on the SEi, a one-tailed Students t-test was used to calculate the P-value of enrichment in stage i (Test if Mi>0). The T statistic was constructed as T=Mi/SEi (df=N-K). Mi>0 and enrichment P<0.001 were used as the threshold of enrichment for each stage. |
WBPaper00035084:L1_enriched_AIN-2_IP
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miRNA targets that are significantly enriched at L2 larva stage. To generate a global view of the dynamics of miRNA-mediated regulation of gene expression during C. elegans development, authors analyzed the mRNAs in the AIN-2-GFP IP results from five developmental stages. The magnitude of the combined interaction of miRNAs with a given target mRNA was assessed by measuring the fold enrichment of that mRNA in AIN-2 IP samples, relative to the abundance of the mRNA in the corresponding total lysate. Because this enrichment in the IP sample versus total lysate directly reflects the miRISC-associated fraction of a given mRNA, high enrichment indicates the likelihood of strong miRNA-mediated regulation of the mRNA, whereas low or negative enrichment indicates the likelihood of weak or absent miRNA regulation of the mRNA. It is also possible that poor enrichment could reflect interactions that occur only in a rare subset of cells at any given stage of development. Transcripts that were significantly enriched (0
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For each transcript represented on the microarray, authors first used all 18 data points from all of the 18 microarrays to calculate its average in-stage standard deviation as SD=SQRT((i=1-K (ni-1)SDi2)/(N-K)), degree of freedom (df)=N-K, where K is the number of developmental stages in which the given transcript had at least one non-missing log2(IP/Total) value; ni is the number of non-missing values in stage i among the K stages; SDi is the standard deviation of the log2(IP/Total) values from all the replicates of stage i; N is the total number of non-missing values for this transcript at all stages. A transcript must have at least one stage with at least two non-missing values to be testable. All of the non-missing values of a transcript at each stage were averaged to generate the stage-average values (Mi for stage i). The standard error of Mi was calculated as SEi=SD/SQRT(ni) (df=N-K), where SD is the average in-stage standard deviation calculated above and ni is the number of non-missing values at stage i, as explained above. Based on the SEi, a one-tailed Students t-test was used to calculate the P-value of enrichment in stage i (Test if Mi>0). The T statistic was constructed as T=Mi/SEi (df=N-K). Mi>0 and enrichment P<0.001 were used as the threshold of enrichment for each stage. |
WBPaper00035084:L2_enriched_AIN-2_IP
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miRNA targets that are significantly enriched at L4 larva stage. To generate a global view of the dynamics of miRNA-mediated regulation of gene expression during C. elegans development, authors analyzed the mRNAs in the AIN-2-GFP IP results from five developmental stages. The magnitude of the combined interaction of miRNAs with a given target mRNA was assessed by measuring the fold enrichment of that mRNA in AIN-2 IP samples, relative to the abundance of the mRNA in the corresponding total lysate. Because this enrichment in the IP sample versus total lysate directly reflects the miRISC-associated fraction of a given mRNA, high enrichment indicates the likelihood of strong miRNA-mediated regulation of the mRNA, whereas low or negative enrichment indicates the likelihood of weak or absent miRNA regulation of the mRNA. It is also possible that poor enrichment could reflect interactions that occur only in a rare subset of cells at any given stage of development. Transcripts that were significantly enriched (0
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For each transcript represented on the microarray, authors first used all 18 data points from all of the 18 microarrays to calculate its average in-stage standard deviation as SD=SQRT((i=1-K (ni-1)SDi2)/(N-K)), degree of freedom (df)=N-K, where K is the number of developmental stages in which the given transcript had at least one non-missing log2(IP/Total) value; ni is the number of non-missing values in stage i among the K stages; SDi is the standard deviation of the log2(IP/Total) values from all the replicates of stage i; N is the total number of non-missing values for this transcript at all stages. A transcript must have at least one stage with at least two non-missing values to be testable. All of the non-missing values of a transcript at each stage were averaged to generate the stage-average values (Mi for stage i). The standard error of Mi was calculated as SEi=SD/SQRT(ni) (df=N-K), where SD is the average in-stage standard deviation calculated above and ni is the number of non-missing values at stage i, as explained above. Based on the SEi, a one-tailed Students t-test was used to calculate the P-value of enrichment in stage i (Test if Mi>0). The T statistic was constructed as T=Mi/SEi (df=N-K). Mi>0 and enrichment P<0.001 were used as the threshold of enrichment for each stage. |
WBPaper00035084:L4_enriched_AIN-2_IP
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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 GR1307[daf-16(mgDf50)] starved and GR1307[daf-16(mgDf50)] 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_GR1307
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Genes with variation in expression level across conditions (control, 25C, High-pH-Salt, Liquid, infection). |
two-way ANOVA |
WBPaper00041174:environmental
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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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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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Genome-wide analysis of developmental and sex-regulated gene expression profile. |
self-organizing map |
cgc4489_group_20
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Genes with significant variation in expression level only across environments(control, 25C, High-pH-Salt, Liquid, infection), but no genotypic variation (AB2, CB4856, RC301, CB4857, N2, HC445). |
two-way ANOVA |
WBPaper00041174:environmental_prime
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The cluster contains genes that showed expression changes in the let-60(G12V) time course that were different than those in the wild-type time course. |
A mixed procedure analysis of variation (ANOVA) was used to identify genes with significantly different expression levels (P < 0.001). |
[cgc5376]:let-60(G12V)-regulated_genes
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Treatment with 0.2mM of HuminFeed until older adult stage (11 days). |
Gene significantly up-regulated by treatment with 0.2mM 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_0.2mM_Up
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Transcripts that showed significantly decrreased expression after 24 hours of exposure to nematicide cyclobutrifluram. |
DESeq2, fold change > 2, FDR <= 0.001. |
WBPaper00066118:cyclobutrifluram_downregulated
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