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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 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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Transcripts that showed significantly altered expression after 24 hour exposure to nitroguanidine (NQ). |
Multivariate permutation tests with random variance model implemented in BRB-Array Tools version 4.5 were performed to infer differentially expressed genes (DEGs). One thousand random permutations were computed per chemical class (i.e., a group of 16 arrays or samples). The confidence level of false discovery rate assessment was set at 80%, and the maximum allowed portion of false-positive genes was 10%. |
WBPaper00055899:nitroguanidine_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 second UVC dose (24h). |
Genes differentially expressed in control vs under EtBr treatment without UVC exposure, at the -25h 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_24h
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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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heat shock |
Genes regulated by heat shock. |
Differences between treatments were visualized by principal component analysis (PCA) plotting with MeV/TM4. Data were initially filtered out for missing values and then subjected to a CLEAR test that combines differential expression and variability using the GEPAS web server at http://www.gepas.org. In our case, the false discovery rate was set to a stringent level of 5 per cent. |
WBPaper00035227:heat_shock_regulated
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Genes with expression 1.5X depleted in PVD and OLL neurons. |
Data sets were normalized by RMA and transcripts showing relative PVD enrichment (>=1.5X) vs. the reference sample were identified by SAM analysis (False Discovery Rate, FDR < 1%) |
WBPaper00036375:depleted_in_PVD_OLL
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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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Down-regulated genes (fold change > 1.5) in two CoQ-deficient clk-1 mutant strains (e2519, qm30) compared to wild types N2. |
Fold-changes of intensities were calculated from the arithmetic mean of gene expression values between experimental and corresponding control group. Fold change >= 1.5 was used as cut-off. |
WBPaper00045774:clk-1_downregulated
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Genes that showed significantly changed expression in daf-16(mgDF50) starved vs N2 starved 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:daf-16(mgDF50)_regulated_Starved
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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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Genes with significantly decreased 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)_downregulated_in-DMSO
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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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Genes that showed significantly decreased expression after exposure to adsorbable organic bromine compounds (AOBr) contained in M. aeruginosa batch culture. |
Differentially expressed genes (DEGs) were identified with a random variance t-test and a significance analysis of microarrays (SAM) test. Genes were considered statistically significant if their p-value was less than 0.05, the false discovery rate less than 0.3, and the fold change compared to control at least <= 0.67 or >=1.5. |
WBPaper00046853:AOBr_M.aeruginosa-batch-culture_downregulated
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Genes that showed significantly decreased expression after exposure to 1mg/L MWCNTs from L1 larva to young adult. |
Transcripts with false discovery rate-corrected p-values < 0.05 and fold change > 2 were defined as differentially expressed. |
WBPaper00049377:MWCNT_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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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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Genes down-regulated after 200 um Quercetin treatment. Fold change < 0.8. |
GCRMA |
WBPaper00040963:Q200_down
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Fungi infection: Candida albicans, heat-killed C. albicans versus heat-killed E. coli. |
Differentially expressed genes in the following exposure comparison :heat-killed C. albicans versus heat-killed E. coli. |
Data were analyzed using Resolver Gene Expression Data Analysis System, version 5.1 (Rosetta Inpharmatics). Three biologic replicates per condition were normalized using the Resolver intensity error model for single color chips. Conditions were compared using Resolver to determine the fold change between conditions for each probe set and to generate a P value using a modified t-test. Probe sets were considered differentially expressed if the fold change was 2-fold or greater (P < 0.01). When comparing datasets, the overlap expected by chance alone was determined in 50 groups of randomly selected C. elegans genes using Regulatory Sequence Analysis Tools (http://rsat.ulb.ac.be/rsat/), a technique that has been used for similar analyses. P values were determined using chi-square tests. |
WBPaper00039851:HK_C_albicans_vs_HK_OP50
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Fasting |
Transcripts that were up regulated by fasting. |
N.A. |
WBPaper00050538:Fasting_upregulated
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Transcripts that showed significantly decreased expression after synchronized L1 larva stage animals were exposed to 1 |
Student's t-tests, fold change > 2, p-value < 0.05. |
WBPaper00055435:MUA-AuNP-0.5_downregulated
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Transcripts that showed significantly decreased expression after synchronized L1 larva stage animals were exposed to 3 |
Student's t-tests, fold change > 2, p-value < 0.05. |
WBPaper00055435:MUA-AuNP-3_downregulated
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Fasting |
Transcripts that were up regulated by fasting in a cholesterol-dependent manner |
N.A. |
WBPaper00050538:Fasting_upregulated_cholesterol-dependent
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Hypoxia treatment 0.5% oxygen for 2 hours. |
Transcriptst that showed significantly increased expression by short-term hypoxia in N2. |
Differentially expressed pro-besets were defined as q-value <= 0.05 and fold change >=1.6. |
WBPaper00066920:hypoxia_upregulated
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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_L3
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feeding/starvation |
The third of four clusters of genes up-regulated during L1 arrest. |
For each average expression value, the larger of the model-based error and empirical error was reported. ANOVA and T-tests were also computed in Rosetta Resolver using the reported errors. Expression values, errors, and P-values corresponding to transcript detection, ANOVAs, and T-tests were exported from Rosetta Resolver and analyzed elsewhere. |
WBPaper00032948:StarveUp3
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Genes with expression altered >= 3-fold in osm-8(n1518) 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:osm-8_regulated
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Bacteria infection: Enterococcus faecium E007 |
Transcripts that showed significantly decreased 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_downregulated
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