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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 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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Genes downregulated 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_downregulated
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Embryonic A-class motor neuron 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_A_Class
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Genes with expression level regulated by genotype (N2 vs CB4856) at L3 larva stage |
Authors permuted transcript values and used a genome-wide threshold of log10 P-value = 2, which resembles a false discovery rate (FDR) of 0.0129. |
WBPaper00040858:eQTL_regulated_juvenile
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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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control(maintained under normal lab light (mostly dark, in incubators).) vs EtBr-exposed(maintained under normal lab light (mostly dark, in incubators) and exposed to EtBr (5ug/mL in agar).) at just prior to the third UVC dose (48h). |
Genes differentially expressed in control vs under EtBr treatment without UVC exposure, at the -1h timepoint. |
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_EtBr-exposed_48h
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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 third UVC dose (48h). |
Genes differentially expressed in control vs after UVC exposure and 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:control_vs_UVC-EtBr-exposed_48h
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Expressed transcripts enriched in embryonic motor neurons (identified by unc-4::GFP expressing cells). |
Comparisons of RMA normalized intensities for unc-4::GFP vs reference cells were statistically analyzed using Significance Analysis of Microarrays software (SAM, Stanford). A two-class unpaired analysis of the data was performed to identify genes that differ by 1.7-fold from the wildtype reference at a False Discovery Rate (FDR) of 1%. These genes were considered significantly enriched. |
WBPaper00025141:unc-4::GFP_Enriched_Genes
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Transcripts with significantly increased 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_upregulated
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Transcripts that showed significantly decreased expression in animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection. |
DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1. |
WBPaper00066146:germline-inx-14(RNAi)_downregulated_PA14
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Transcripts that showed significantly decreased expression in hda-2(ok1479) comparing to in N2 animals. |
DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2. |
WBPaper00062159:hda-2(ok1479)_downregulated
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Feeding for 4 hours after L1 arrest. |
Transcripts that showed significantly increased expression after 4 hours of feeding of starvation-induced arrested L1 N2 animals, comparing to animals continue to starve. |
DESeq2, FDR < 0.05, fold change > 2. |
WBPaper00067518:food_upregulated_N2
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Proteins detected in gonad from single-worm studies. |
N.A. |
WBPaper00066880:gonad_expressed
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Proteins detected in intestine from single-worm studies. |
N.A. |
WBPaper00066880:intestine_expressed
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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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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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Transcriptions that showed significantly decreased expression in skn-1(RNAi) comparing to empty vector injection into rrf-3(pk1426);daf-2(e1368) animals. |
Genes with an absolute fold changeof at least 2 and standard p-values below 0.05 were considered as differentially expressed. |
WBPaper00062193:skn-1(RNAi)_downregulated
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Genes down-regulated after 200 um Quercetin treatment. Fold change < 0.8. |
GCRMA |
WBPaper00040963:Q200_down
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Genes from N2 animals with significantly increased expression after 72 hours of treatment on growth media with 250uM allantoin 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_allantoin_upregulated
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Genes enriched 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_enriched
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Total muscle enriched genes (complete list of non-overlapping genes from the 0hr and 24hr muscle enriched 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_enriched
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Feeding for 4 hours after L1 arrest. |
Transcripts that showed significantly increased expression after 4 hours of feeding of starvation-induced arrested L1 rsks-1(ok1255) animals, comparing to animals continue to starve. |
DESeq2, FDR < 0.05, fold change > 2. |
WBPaper00067518:food_upregulated_rsks-1(ok1255)
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FBF-associated probe sets (FDR <2.25%) |
SAM assigns a score to each probe set and estimates their false discovery rates (FDRs). SAM deemed 4722 probe sets as significantly enriched at an FDR of 2.25% or lower. |
WBPaper00035905:FBF-1_Associated
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4 hours of starvation. |
Genes with significantly decreased expression in N2 animals after 4 hours of starvation. |
Differentially expressed genes were determined by ANOVA analysis using the Partek software package. |
WBPaper00047070:N2_starvation_downregulated
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Genes showing > 1.5-fold up-regulated expression (p<0.001) both in aex-3::His-SUMO-1 and myo-4::His-SUMO-1 C. elegans. |
The Linear Models for Microarray Data (Limma) package using linear model fitting for statistical testing with empirical Bayes variance smoothing procedure were applied to detection of differentially expressed genes in aex-3::His-SUMO-1 and myo-4::His-SUMO-1 nematodes when compared to N2. The obtained p values were corrected for multiple testing using Benjamini and Hochberg false discovery rate procedure. For downstream analysis, genes with FDR corrected p < 0.001 were used including 1,805 probe sets from aex-3::His-SUMO-1 versus N2 comparison (899 under- and 906 overexpressed) and 1,342 probe sets from myo-4::His-SUMO-1 versus N2 comparison (774 under and 568 overexpressed). |
WBPaper00038060:SUMO-1_upregulated
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Transgenic human alpha-Synuclein(WT) |
Genes upregulated by transgenic human alpha synuclein (WT) at least 2 fold comparing with control. |
t-test, p < 0.05 |
WBPaper00027342:alpha-Synuclein(WT)_upregulated
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Oxidative stress. |
Genes downregulated by oxidative stress. |
Assessed by SAM (Significance Analysis of Microarray) [false discovery rate (FDR) = 11%] |
WBPaper00034757:down_by_oxidative_stress
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Genome-wide analysis of developmental and sex-regulated gene expression profile. |
self-organizing map |
cgc4489_group_4
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C-lineage related expression profile. |
QT clustering |
WBPaper00025032:cluster_30
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