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Bacteria: E.faecalis strain OG1RF |
Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF. |
Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05. |
WBPaper00059754:E.faecalis_OG1RF_upregulated
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Coexpression clique No. 60, 176662_at-Y53F4B.16, 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. |
WBPaper00061527:176662_at-Y53F4B.16
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Genes with expression level regulated by genotype (N2 vs CB4856) 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_regulated_developing
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Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage. |
DESeq2 version 1.22.2, p < 0.05 |
WBPaper00064716:paraquat_downregulated
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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 increased expression in daf-2(e1370) comparing to in N2. |
Student's t-test, fold change > 2, p-value < 0.05. |
WBPaper00055386:daf-2(e1370)_upregulated
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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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Transcripts that showed significantly decreased expression after animals grew in 500 uM glycine from hatch till 1-day post L4 adult, comparing to untreated animals. |
Differential expression was assessed using a nempirical Bayes moderated t-test within limmas linear model framework including the precision weights estimated by voom.Resulting p-values were corrected for multiple testing using the Benjamini-Hochberg false discovery rate. Curator applied threshold: fold change > 2, adjusted p-value < 0.01. |
WBPaper00056330:glycine_downregulated
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Transcripts that showed significantly decreased expression in eat-2(ad465);dve-1(RNAi) animals comparing to eat-2(ad465) animals injected with empty vector. |
fold change > 2, FDR < 0.01 |
WBPaper00067391:dve-1(RNAi)_downregulated_eat-2(ad465)
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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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Genes that showed significant differential expressed between control and 150 mg\/L Atrazine treatment. |
t-test, p < 0.05. |
WBPaper00036123:Atrazine_regulated
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Transcripts that showed significantly increased expression in uthIs235 [sur-5p-hsf-1-unc-54 3'UTR + myo-2p-tdTomato-unc-54 3' UTR] comparing to in N2. |
DESeq2 FDR < 0.05, fold change > 2. |
WBPaper00067474:HSF-1(OverExpress)_upregulated
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Genes from N2 animals with significantly decreased 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_downregulated
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Bacteria: B.subtilis |
Transcripts that showed significantly increased expression when animals were fed by probiotic bacteria strain B.subtilis PXN21 comparing to animals fed with OP50 from L1 till day 1 adult. |
edgeR 3.16.5, FDR < 0.05, fold change > 2. |
WBPaper00059117:B.subtilis_upregulated
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Transcripts that showed significantly increased expression in diploid N2 animals after exposure to 5 uM doxorubicin for 72 hours at 15C from L1 to L4 larve stage. |
DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05. |
WBPaper00066110:Doxorubicin_upregulated_diploid
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Transcripts that showed significantly increased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage. |
DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05. |
WBPaper00066110:tetraploid_vs_diploid_upregulated
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Fungi infection: Drechmeria coniospora |
Genes with decreased 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_downregulated_RNAseq
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Transcripts that showed significantly increased expression in hlh-26(ok1453) animals exposed to E. faecium for 8 hours, comparing to N2 animals exposed to E. faecium for 8 hours. |
Fold change > 2. |
WBPaper00062585:hlh-26(ok1453)_upregulated_E.faecium
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Germline-enriched and sex-biased expression profile cluster D. |
hierarchical clustering |
[cgc6390]:Cluster_D
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spermatogenesis-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]:spermatogenesis-enriched
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Transcripts that showed significantly decreased expression in unc-30(ok613) animals at L4 larva stage, comparing to N2 animals. |
Genes exhibiting at least two-fold change were considered differentially expressed. |
WBPaper00061439:unc-30(ok613)_downregulated
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Transcripts that showed significantly decreased expression in flcn-1(ok975) comparing to in N2. |
Student's t-test. |
WBPaper00056471:flcn-1(ok975)_downregulated
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Transcripts that showed significantly decreased expression in BAT525 [hmg-3 (tm2539) / dpy-5(e61) unc-13(e1091) I.] comparing to in N2 at 1-day post L4 adult hermaphrodite stage |
DESeq 2, fold change > 4, adjusted p-value < 0.05. |
WBPaper00055013:hmg-3(bar24)_downregulated
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Transcripts enriched in male him-5(e1490 animals, comparing to in N2 hermaphrodite animals from L3 larva to young adult stages. |
DESeq FDR < 0.01. |
WBPaper00050231:male_enriched
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Transcripts that showed significantly increased expression in animals with pan-neuronal expression of human amyloid beta (snb-1p-Amyloid-beta(1-42) + mtl-2p-GFP), comparing to in N2 animals. |
edgeR p-value < 0.01 and fold change > 4. |
WBPaper00061613:human-amyloid-beta_upregulated
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Transcripts that showed significantly increased expression in eat-2(ad465) comparing to in N2. |
Student's t-test, fold change > 2, p-value < 0.05. |
WBPaper00055386:eat-2(ad465)_upregulated
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Bacteria infection: Staphylococcus epidermidis |
Transcripts that showed significantly increased expression in mab-5(e1239) animals exposed to S. epidermidis for 24 hours since L4 larva stage, comparing to uninfected mab-5(e1239) animals. |
DESeq2, (FDR)-adjusted P-value < 0.05 and fold change >= 2. |
WBPaper00066587:S.epidermidis_upregulated_mab-5(e1239)
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Transcripts that showed significantly increased expression in skn-1(lax188);daf-2(e1370) comparing to in skn-1(lax188) animals |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00067765:daf-2(e1370)_upregulated_skn-1(lax188)
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Transcripts that showed significantly increased expression in N2 comparing to in skn-1 gain of function allele lax188 animals |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00067765:skn-1(lax188)_downregulated_N2
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Transcripts that showed significantly increased expression in N2 animals growing in 15mg per mL doxycycline from L1 to L4 larva stage. |
edgeR (version 3.24.3), fold change > 4, FDR < 0.01. |
WBPaper00062456:doxycycline_upregulated_N2_transcript
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