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Bacteria infection: Enterococcus faecalis |
Genes with increased expression after 24 hours of infection by E.faecalis Fold changes shown are pathogen vs OP50. |
For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated. |
WBPaper00038438:E.faecalis_24hr_upregulated_TilingArray
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Coexpression clique No. 203, sre-33-ZK1025.1_8337, on the genome-wide coexpression clique map for the nematode GPL200 platform. |
All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform. |
WBPaper00061527:sre-33-ZK1025.1_8337
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Genes with expression level regulated by genotype (N2 vs CB4856) and age at L3 larva and Late reproduction stage (96 hours at 24 centigrade). |
For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR). |
WBPaper00040858:eQTL_age_regulated_developing
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Transcripts that showed significantly increased expression in hda-1(ne4752[3xFLAG-Degron-HDA-1]) in gonads dissected from 1-day old adult animals. |
Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. |
WBPaper00061479:hda-1(ne4752)_upregulated
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Transcripts that showed significantly increased expression in mep-1(ne4629[MEP-1-GFP-Degron]) in gonads dissected from 1-day old adult animals. |
Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. |
WBPaper00061479:mep-1(ne4629)_upregulated
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Transcripts that showed significantly increased expression in ubc-9(ne4833[ubc-9(G56R)] in gonads dissected from 1-day old adult animals. |
Salmon was used to map the mRNA-seq reads with the worm database WS268, and its output files were imported to DESeq2 in R. The differentially expressed genes were filtered by fold change more than 2 and adjusted p-value < 0.05. The scatter plots were generated by the plot function in R. |
WBPaper00061479:ubc-9(ne4833)_upregulated
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Transcripts that showed significantly decreased expression in hpl-2(tm1489) comparing to in N2 animals. |
DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2. |
WBPaper00054493:hpl-2(tm1489)_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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Heat shock: 34C 30min. |
Transcripts that showed significantly increased expression in L2 larva stage C. elegans animals after incubated in a 34C water bath for 30min. |
DESeq2 v 1.18.1, fold change > 2, FDR < 0.01. |
WBPaper00058955:heatshock_upregulated_CE
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Transcripts of coding genes that showed significantly increased expression in muscle. |
DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed. |
WBPaper00062325:muscle_enriched_coding-RNA
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Transcripts that showed significantly increased expression in cfp-1(tm6369) comparing to in N2 at early embryo stage. |
DESeq2, FDR < 0.05 |
WBPaper00058691:cfp-1(tm6369)_upregulated
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Transcripts that showed significantly increased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals. |
DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. |
WBPaper00060014:set-2(tm1630)_upregulated
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Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2 at early embryo stage. |
DESeq2, FDR < 0.05 |
WBPaper00058691:sin-3(tm1276)_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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Transcripts that showed significantly increased expression in Day 5 (5-days post-L4) vs. Day 0 (L4 larva) of adulthood N2 animals. |
Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method. |
WBPaper00053318:Aging_upregulated_mRNA_N2
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Significantly downregulated genes from cyc-1(RNAi) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips. |
SAM algorithm with an FDR < 0.1. |
WBPaper00033065:cyc-1(RNAi)_downregulated
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Genes regulated by spr-5 (greater than 2-fold change between spr-5(by101) generations 1, 13, and 26). |
Significantly differentially regulated genes were selected by using a 2-fold ifference along with intensity values > 1000. |
WBPaper00033101:spr-5_regulated
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Genes with differential expression under 1.0mg/l Diazinon treatment at 16 centigrade. |
To identify the differentially expressed genes in each treatment authors used linear models per toxicant and temperature (gene expression = Toxicant (effect) + error). The lm function in R stats package was used to implement the linear models analysis with recommended default options. For threshold determination authors used a permutation approach. For each of the 23,232 permutations used authors randomly picked a transcript (array spot), which could only be picked once. Authors combined all the expression values of this transcript and randomly distributed them over the replicates and used them in the linear model. In this way authors obtained a threshold for each of the toxicants. Authors used a -log10 p-value 2 as common threshold for the analysis, which resembles to the following FDR per toxicant: 0.0155 for CPF at 24 centigrade, 0.0148 for DZN at 24 centigrade, 0.0168 for CPF+DZN at 24 centigrade, 0.0142 for CPF at 16 centigrade, 0.0151 for DZN at 16 centigrade, and 0.0148 for CPF+DZN, at 16 centigrade. |
WBPaper00037113:Diazinon_16C_regulated
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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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Bacteria infection: Bacillus thurigiensis DB27 |
Caenorhabditis elegans Genes with expression levels changed significantly after treatment of Bacillus thurigiensis DB27. |
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_B.thuringiensis-DB27_regulated
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Transcripts that did not alter expression in smg-1(r910) and smg-1(r910) smg-2(r915) mutants comparing to in N2, but their mRNAs co-purify with SMG-2. |
edgeR |
WBPaper00053308:SMG-2_associated_NMD(-)_unaltered_ClassII
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Genes that showed decreased expression after germline ablation comparing to un-ablated animals. |
The differential expression between germline-ablated versus gonad-ablated animals was computed via the functions makeContrasts and contrasts.fit in the limma package in R/Bioconductor. |
WBPaper00045571:germline-ablation_downregulated
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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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Fungi infection: Drechmeria coniospora |
Genes with increased expression after 12 hours of infection by D.coniospora Fold changes shown are pathogen vs OP50. |
For RNA-seq and tiling arrays, log2 fold changes between gene expression values of infected versus uninfected nematodes were calculated. For log2 fold changes > 0.00001 the values > 81.25th percentile were defined as up-regulated and for log2 fold changes < -0.00001 the values < 18.75th percentile were defined as down-regulated. |
WBPaper00038438:D.coniospora_12hr_upregulated_RNAseq
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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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Transcripts that showed significantly increased expression in set-2(bn129) comparing to in N2 at early embryo stage. |
DESeq2, FDR < 0.05 |
WBPaper00058691:set-2(bn129)_upregulated
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Transcripts that showed differential expression in adult N2 vs adult mir-34(OverExpression) animals at 25C. |
N.A. |
WBPaper00050488:N2_vs_mir-34(OverExpression)_regulated_adult_25C
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Transcripts that showed differential expression in adult mir-34(gk437) vs adult mir-34(OverExpression) animals at 25C. |
N.A. |
WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_adult_25C
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Targets of endo-siRNA that showed significantly increased expression in BFF39[pptr-1(tm3103);Pmex-5::gfp::h2b::tbb-2 (mjIs134 II)] comparing to in SX1263[Pmex-5::gfp::h2b::tbb-2 (mjIs134 II)] dissected gonad isolated from 1-day old adult hermaphrodites. |
DESeq2, fold change > 2, FDR < 0.01 |
WBPaper00057140:pptr-1(tm3103)_upregulated
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Expression Pattern Group F, enriched for genes involved in embryonic development. These patterns have in common that they all have genes of which the expression goes up after the juvenile stage. The expression of the genes in these patterns remains high or even goes up after reproduction. |
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_F
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