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Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells. |
DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. |
WBPaper00060811:L1_vs_adult_upregulated_neural
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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 Rapamycin and 50uM Rifampicin from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Rapamycin-Rifampicin_downregulated
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Transcripts that showed significantly decreased 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_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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Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00066594:ilc-17.1(syb5296)_upregulated
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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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Genes regulated by DAF-12, according to whole transcriptome profiling to compare genome-wide regulatory influences of DPY-21 and SET-4 to those of the key transcription factors controlling dauer arrest in eak-7;akt-1 animals, DAF-16 and DAF-12. |
Authors identified genes differentially expressed between wild-type and eak-7;akt-1 double mutant animals [fold change >= 1.5 and false discovery rate (FDR) < 0.05]. Authors then compared the transcriptomes of eak-7;akt-1 double mutants to those of eak-7;akt-1 animals harboring mutations in dpy-21, set-4, daf-16, or daf-12, and identified genes that are differentially expressed in the opposite direction as in wild-type relative to eak-7;akt-1. Annotated gene expression data output from CuffDiff v2.2.1 was read into R version 3.2.1 for six comparisons: eak-7;akt-1 compared to (1) wild-type, (2) daf-16(mu86);eak-7;akt-1, (3) daf-12;eak-7;akt-1, (4) set-4(n4600);eak-7;akt-1, (5) set-4(dp268);eak-7;akt-1, and (6) dpy-21;eak-7;akt-1. Authors filtered genes by the following criteria: (1) status = OK for wild-type vs. eak-7;akt-1, (2) fold change (FC) >= 1.5 or FC <= 1/1.5 for wild-type vs. eak-7;akt-1 and (3) FDR < 0.05 for at least two separate comparisons. |
WBPaper00050801:DAF-12_dauer_regulome
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Genes regulated by DAF-16, according to whole transcriptome profiling to compare genome-wide regulatory influences of DPY-21 and SET-4 to those of the key transcription factors controlling dauer arrest in eak-7;akt-1 animals, DAF-16 and DAF-12. |
Authors identified genes differentially expressed between wild-type and eak-7;akt-1 double mutant animals [fold change >= 1.5 and false discovery rate (FDR) < 0.05]. Authors then compared the transcriptomes of eak-7;akt-1 double mutants to those of eak-7;akt-1 animals harboring mutations in dpy-21, set-4, daf-16, or daf-12, and identified genes that are differentially expressed in the opposite direction as in wild-type relative to eak-7;akt-1. Annotated gene expression data output from CuffDiff v2.2.1 was read into R version 3.2.1 for six comparisons: eak-7;akt-1 compared to (1) wild-type, (2) daf-16(mu86);eak-7;akt-1, (3) daf-12;eak-7;akt-1, (4) set-4(n4600);eak-7;akt-1, (5) set-4(dp268);eak-7;akt-1, and (6) dpy-21;eak-7;akt-1. Authors filtered genes by the following criteria: (1) status = OK for wild-type vs. eak-7;akt-1, (2) fold change (FC) >= 1.5 or FC <= 1/1.5 for wild-type vs. eak-7;akt-1 and (3) FDR < 0.05 for at least two separate comparisons. |
WBPaper00050801:DAF-16_dauer_regulome
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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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Genome-wide analysis of developmental and sex-regulated gene expression profile. |
self-organizing map |
cgc4489_group_12
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Transcripts that showed significantly increased expression in zip-3(gk3164) comparing to in N2, after exposed to P. aeruginosa for 18 hours. |
p < 0.05 |
WBPaper00056326:zip-3(gk3164)_upregulated_P.aeruginosa-infected
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Transcripts that showed differential expression between 24 and 26 hours post hatching L2d and dauer committed larvae of daf-9(dh, triggered by the dafachronic acid (DA) growth hormone6). Cluster 2 genes' expression gradually increased into dauer. |
Benjamini Hochberg corrected q-value < 0.01. |
WBPaper00053388:dauer_regulated_Cluster2
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Transcripts that showed significantly increased exression in animals exposed to 100uM cadmium for 24 hours. |
DESeq2 v1.20.0, fold change > 2, FDR < 0.05. |
WBPaper00065029:cadmium_upregulated
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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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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).) vs UVC-exposed(exposed to 7.5 J/m2 UVC radiation 3 times, 24 h apart (48 h total).) at just prior to the third UVC dose (48h). |
Genes differentially expressed under EtBr treatment and UVC exposure vs under UVC exposure but without 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:UVC-EtBr-exposed_vs_UVC-exposed_48h
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Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin, 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:Rapamycin-Rifampicin-Allantoin_downregulated
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Transcripts depleted in Q cell. |
DESeq2 (version 2.11.40.7) FDR < 0.05, fold change > 2. |
WBPaper00066652:Q-cell_depleted
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Transcripts that showed altered expression in cat-2(RNAi) animals comparing to control animals injected with empty vector. |
p-value <= 0.05 |
WBPaper00066902:cat-2(RNAi)_regulated
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Transcripts that showed significantly decreased expression in day 1 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. |
Fold change > 2, FDR < 0.05 |
WBPaper00064088:Day-1-adult_vs_L4_downregulated_fem-3(q20)
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Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva fem-3(q20) animals. |
Fold change > 2, FDR < 0.05 |
WBPaper00064088:Day-3-adult_vs_L4_downregulated_fem-3(q20)
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Genes up regulated in the dauer versus dauer-exit worms. |
The weight parameters were optimized based on MA-plots such that spike-in controls show their expected fold change values. lmFit function was used to fit a linear model to probe intensities across arrays, and differential expression was calculated by empirical Bayes method using the eBayes function. Control of FDR was employed as correction for multiple testing. |
WBPaper00041207:CE_dauer_up
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Feeding for 4 hours after L1 arrest. |
Transcripts that showed significantly decreased expression after 4 hours of feeding of starvation-induced arrested L1 N2 animals, comparing to animals continue to starve. |
DESeq2, FDR < 0.05, fold change > 2. |
WBPaper00067518:food_downregulated_N2
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Feeding for 4 hours after L1 arrest. |
Transcripts that showed significantly decreased expression after 4 hours of feeding of starvation-induced arrested L1 rsks-1(ok1255) animals, comparing to animals continue to starve. |
DESeq2, FDR < 0.05, fold change > 2. |
WBPaper00067518:food_downregulated_rsks-1(ok1255)
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Drug treatment: Elbe sediment |
Genes with significantly changing transcripts in C. elegans exposed to the Elbe (E) sediment. |
[ANOVA, p < 0.05 without multiple sample correction, fold-change to reference sediment Danube (D) > 1.4 (up-regulated) or < 0.7 (down-regulated)]. |
WBPaper00033070:Elbe_upregulated
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Transcripts that showed significantly increased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector. |
DESeq2. FDR < 0.05. |
WBPaper00060459:bcat-1(RNAi)_upregulated
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Transcripts that showed significantly increased expression in alg-1(gk204) comparing to in N2 at 5-days post L4 adult hermaphrodites. |
DESeq, fold change > 2, adjusted p-value < 0.05. |
WBPaper00054758:alg-1(gk204)_upregulated
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Single-cell RNA-Seq cell group 74_0 expressed in neuron. |
scVI 0.6.0 |
WBPaper00065841:74_0
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Single-cell RNA-Seq cell group 109_0 expressed in neuron. |
scVI 0.6.0 |
WBPaper00065841:109_0
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Heat shock: 35C for 1 hour. |
Transcripts that showed significantly decreased expression immediately after 1-day post L4 adult hermaphrodite endu-2(tm4977) animals were exposed to 35C for 1 hour. |
The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01. |
WBPaper00065749:Heat-Shock_downregulated_endu-2(tm4977)
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