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mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis. |
Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05. |
WBPaper00045420:fertilization_downregulated_transcript
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Osmotic stress |
Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present |
DESeq(version 1.10.1), FDR < 0.05. |
WBPaper00050726:OsmoticStress_regulated_Food
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Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals. |
Fold change > 2, FDR < 0.01. |
WBPaper00065993:glp-1(e2141)_upregulated
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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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Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Rifampicin-Allantoin_upregulated
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Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Rapamycin-Metformin_upregulated
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Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging. |
Cufflinks FPKM value >=1. |
WBPaper00050990:body-muscle_expressed
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Transcripts that showed significantly decreased expression in dissected female germline comparing to in dissected male germline. |
Log2 Fold change > 2 or <-1, p-value < 0.05. |
WBPaper00053599:female_vs_male_downregulated
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Transcripts that showed significantly decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:eat-2(ad1116)_downregulated
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Transcripts that showed significantly decreased expression after animals were treated with 100uM Psora from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Psora_downregulated
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Bacteria: B.thuringiensis |
Transcripts in elt-2(RNAi) animals that were significantly differentially expressed at least for one time point and one pathogenic strain Bt247 and Bt679 compared to the non pathogenic strain Bt407. |
Cuffdiff |
WBPaper00060358:B.thuringiensis_pathogen_regulated_elt-2(RNAi)
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Proteins identified in extracellular vesicle. |
N.A. |
WBPaper00062669:extracellular-vesicle_protein
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Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. |
DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. |
WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
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Bacteria infection: Serratia marcescens |
Genes with increased expression after 24 hours of infection by S.marcescens 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:S.marcescens_24hr_upregulated_TilingArray
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Transcripts that showed significantly increased expression in daf-2(e1370) neurons comparing to in N2 neurons at day 8adult stage. |
DESeq2, FDR < 0.05, fold change > 2. |
WBPaper00066978:daf-2(e1370)_upregulated_neuron
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Transcripts that showed significantly increased expression in daf-16(mu86);daf-2(e1370) neurons comparing to in daf-2(e1370) neurons at day 8adult stage. |
DESeq2, FDR < 0.05, fold change > 2. |
WBPaper00066978:daf-16(mu86)_upregulated_neuron
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Bacteria infection: Serratia marcescens |
Genes with increased expression after 24 hours of infection by S.marcescens 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:S.marcescens_24hr_upregulated_RNAseq
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20C vs 25C |
Transcripts that showed differential expression in 20C vs 25C in N2 animals at adult stage. |
N.A. |
WBPaper00050488:20C_vs_25C_regulated_N2_adult
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Genome-wide analysis of developmental and sex-regulated gene expression profile. |
self-organizing map |
cgc4489_group_14
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Genes that showed significantly decreased experssion after 22.5 hours of treatment in 200nM delta7-dafachronic acid comparing with in ethanol vehicle control. |
To identify the differentially expressed genes, we applied Significance Analysis of Microarrays (SAM) analysis using the R package samr [46]. Genes with median false discovery <5% and fold changes >2.0 were considered differentially expressed. |
WBPaper00046548:dafachronic-acid_downregulated
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male soma-enriched |
Comparisons were made between genotypes by subtracting the mean log value of one ratio from another, and the significance of the difference was evaluated using Student t-test for two populations. For the fem-3(gf) versus fem-1(lf) direct comparison, authors performed the same analysis, except they used a Students t-test for one population. Author chose a combination of a twofold difference with a t value exceeding 99% confidence (P < 0.01), because these criteria allowed the inclusion of essentially all genes that had previously been identified as germline-enriched in a wt/glp-4 hermaphrodite comparison. Additionally, requiring a twofold difference reduced false positives, as the number of genes with two-fold difference and a P<0.01 only included ~100 genes more than with P < 0.001, and almost all genes showed germline expression by in situ hybridization. |
[cgc6390]:male_soma-enriched
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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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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 decreased expression in csr-1a(tor159) comparing to in N2 at 25C. |
DESeq2, fold change > 2, p-value < 0.05. |
WBPaper00061753:csr-1(tor159)_downregulated_25C
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Genes eniched in hermaphrodites by comparing tra-2(ar221ts);xol-1(y9) XX phenotype males (at 25C) with either N2 or xol-1(y9) XX hermaphrodites during L4 larva stage |
Student t-test. An mRNA was considered to have sex-enriched expression if it showed at least a two-fold enrichment within a 99% confidence interval (P < 0.01). |
WBPaper00026629:L4_male_enriched
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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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Bacteria infection: Photorhabdus luminescens |
Genes with increased expression after 24 hours of infection by P.lumniescens 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:P.lumniescens_24hr_upregulated_TilingArray
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Transcripts expressed in male vas deferens, according to RNA tomography. |
RNA tomography |
WBPaper00055648:male-vas-deferens_expressed
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Transcripts that showed significantly increased expression in xpf-1(tm2842) comparing to in N2 animals. |
DESeq2 1.14.1, fold change > 2, FDR < 0.01. |
WBPaper00062497:xpf-1(tm2842)_upregulated
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