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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 that showed more than 2 fold increased expression in pmk-1(km25) comparing to in N2 when fed with OP50. |
The significantly expressed genes were selected based on ANOVA analysis by Partek Genomics Suite software. Genes with a p-value of <0.05 and a 2-fold or greater fold change were considered differentially expressed. |
WBPaper00046083:pmk-1(km25)_OP50_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 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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Genes down-regulated after 24 hour exposure to colistin. |
Gene lists were created using a cutoff P-value of < 0.05, 2-fold change. |
WBPaper00045673:colistin_downregulated
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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 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 that significantly decreased expression in dnj-14(ok237) and dnj-14(tm3223) when comparing to either N2 or CZ1200 juIs76 [unc-25p::GFP; lin-15(+)] |
The significance test of the estimated logFC (log2 Fold Change) for each contrast was performed by the empirical Bayes function packed in limma and p-values were adjusted using the Benjamini and Hochberg FDR control approach to deal with the effect of multiple tests. Both 5% and 1% false discovery rate (FDR) datasets were analysed in order to ensure the highest confidence in the observed enriched genes and pathways whist ensuring there was no loss of representation of DEGs at higher stringency levels. At 5% FDR, 3569 DEGs were revealed compared to N2 (Bristol) and 506 DEGs compared to CZ1200. Further analysis of these data identified 50 Up-regulated and 240 down-regulated DEGs which were common to both control strain datasets. |
WBPaper00048567:dnj-14_downregulated
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fasting |
Genes upregulated by fasting anytime during the 48 hour time course in N2 worms. |
Hierarchical clustering analysis was done with squared Euclidean as the distance metric and average linkage as the cluster method by using GeneSpring GX. |
WBPaper00041960:N2_fasting_upregulated_anytime
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Genes down-regulated after 100 um Quercetin treatment. Fold change < 0.8. |
GCRMA |
WBPaper00040963:Q100_down
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Genes down-regulated after 200 um Quercetin treatment. Fold change < 0.8. |
GCRMA |
WBPaper00040963:Q200_down
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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 3 h after the first UVC dose (3h). |
Genes differentially expressed under EtBr treatment without UVC exposure vs after UVC exposure but without EtBr treatment at the -45h timepoint (3 hours after the first UVC dose). |
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_3h
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Genes that showed more than 2 fold increased expression in oga-1(ok1207) comparing to in N2 when fed with OP50. |
The significantly expressed genes were selected based on ANOVA analysis by Partek Genomics Suite software. Genes with a p-value of <0.05 and a 2-fold or greater fold change were considered differentially expressed. |
WBPaper00046083:oga-1(ok1207)_OP50_upregulated
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fasting |
Genes upregulated more than 2-fold by fasting for 48 hours in N2. |
Statistical analysis was performed by two-way analysis of variance (ANOVA) with a Benjamini and Hochberg false discovery rate (BH-FDR-0.1) multiple testing corrections followed by Tukey post hoc tests using log-transformed data (GeneSpring GX). |
WBPaper00041960:N2_fasting_upregulated
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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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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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Genes down-regulated after 300 um Tannic acid treatment. Fold change < 0.8. |
GCRMA |
WBPaper00040963:TA300_down
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24 hours of AgNPs exposure. |
Genes upregulated more than 2 fold after 24 hours of AgNPs exposure. |
Statistical differences between the control and exposed worms were determined by a parametric t test, and a Pearson correlation test was performed for correlation analysis, using the Statistical Package for the Social Sciences (SPSS, Chicago, IL). |
WBPaper00034661:AgNPs_upregulated
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Genes down-regulated after 200 um Tannic acid treatment. Fold change < 0.8. |
GCRMA |
WBPaper00040963:TA200_down
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Genes that showed more than 2 fold increased expression in ogt-1(ok1474) comparing to in N2 when fed with OP50. |
The significantly expressed genes were selected based on ANOVA analysis by Partek Genomics Suite software. Genes with a p-value of <0.05 and a 2-fold or greater fold change were considered differentially expressed. |
WBPaper00046083:ogt-1(ok1474)_OP50_upregulated
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C-lineage related expression profile. |
QT clustering |
WBPaper00025032:cluster_70
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