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Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. |
DESeq. False discovry rate (FDR) < 0.1. |
WBPaper00048988:neuron_expressed
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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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Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. |
N.A. |
WBPaper00064071:NHR-49_interacting
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Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging. |
Cufflinks FPKM value >=1. |
WBPaper00050990:hypodermis_expressed
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Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging. |
Cufflinks FPKM value >=1. |
WBPaper00050990:NMDA-neuron_expressed
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Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva glp-1(e2141) animals. |
Fold change > 2, FDR < 0.05 |
WBPaper00064088:Day-3-adult_vs_L4_downregulated_glp-1(e2141)
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Bacteria infection: Bacillus thuringiensis |
Transcripts that showed significantly increased expression in N2 animals infected by bacteria BMB171/Cry5Ba, an acrystalliferous Bt mutant BMB171 transformed with toxin gene cry5Ba on the shuttle vector pHT304, comparing to N2 animals infected by BMB171/pHT304. |
N.A. |
WBPaper00064229:B.thuringiensis-Cry5Ba_upregulated
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Genes that showed significantly increased expression in daf-2(e1370);hel-1(gk148684) comparing to in hel-1(gk148684) |
To identify DEGs, Students t test and the log2 median ratio test were performed to compute t values and median ratios for all the annotated genes. The adjusted P values from each test were computed using an empirical distribution of the null hypothesis, which was obtained from random permutations of the samples. Finally, the adjusted P values from the individual tests were combined to compute the overall P values using Stouffers method , and genes with overall P < 0.05 and fold change > 1.5 were selected as DEGs. |
WBPaper00047131:daf-2(e1370)_upregulated_hel-1(gk148684)-background
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Transcripts that showed significantly increased expression in daf-2(e1370) comparing to in control animals. |
NOIseq(v2.34.0), fold change > = 1.5, Differentially expressed genes (DEGs) were defined as having a probability of differentialexpression > 95%. |
WBPaper00064727:daf-2(e1370)_upregulated
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Transgeneration hypoxia treatment. |
Transcripts that are significantly upregulated in F1 animals after P0 parents were exposed to 0.1% oxygen for 16 hours at L4 larva stage. |
For calling the significant differentially expressed genes (DEGs),the false discovery rate (FDR) after multiple testing correction was set as 0.05 and analyzed in edgeR. |
WBPaper00064871:hypoxia_upregulated_F1
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Transcripts that showed significantly decreased 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_downregulated_mRNA_N2
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Transcripts that showed significantly decreased expression in mir-71(n4115) comparing to in N2 at 4-days post L4 adult hermaphrodite. |
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:mir-71(n4115)_downregulated_mRNA
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Transcripts depleted in purified oocyte P bodies comparing to in the whole animal. |
DESeq2, FDR < 0.05, fold change > 2. |
WBPaper00065975:P-body_vs_WholeAnimal_depleted
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Genes that showed increased expression after nicotic acid (NA) treatment. |
Raw counts for the genes were analyzed using the R Statistical Computing Environment and the Bioconductor packages DESeq and edgeR. Both packages provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting p-values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate (FDR). If both FDR values (by DESeq and edgeR) were smaller than p = 0.05, genes were assigned as differentially expressed. |
WBPaper00044260:nicotinc-acid_upregulated
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Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy. |
Cufflinks |
WBPaper00065120:body-muscle-transcriptome
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Temprature shift to 28C for 24 hours. |
Transcripts that showed significantly decreased expression after animals were exposed to 28C temperature for 24 hours. |
Differentially expressed genes wereidentified using DESeq (v.1.18.0) by normalizing readsbased on the negative binomial distribution method andcomparing each HS timepoint to the 0-h control. |
WBPaper00061341:28C_24h_downregulated
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Proteins that showed significantly decreased expression after 1-day-old wild type adults were exposed to cisplatin (300ug per mL) for 6 hours. |
The differential expression analysis was performed in R. Differentially expressed proteins were identified by using a two-sided t-test on log-transformed data. |
WBPaper00065373:Cisplatin_downregulated_WT
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Transcripts that showed significantly increased expression in hpk-1(pk1393) comparing to in N2 at adult day 2. |
DESeq 2, fold change > 2, FDR < 0.05. |
WBPaper00065581:hpk-1(pk1393)_upregulated
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Transcripts that showed significantly increased expression in mbl-1(syb4318), referred to as mbl-1short(ex7-), comparing to in N2 at L4 larva stage. |
DESeq2, Fold change > 2 and FDR < 0.05 |
WBPaper00066410:mbl-1(syb4318)_upregulated
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Transcripts that showed significantly increased expression in mbl-1(syb4345), referred to as mbl-1long(ex7+), comparing to in N2 at L4 larva stage. |
DESeq2, Fold change > 2 and FDR < 0.05 |
WBPaper00066410:mbl-1(syb4345)_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 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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Transcripts that showed significantly increased expression in mut-16(pk710), comparing to in N2 animals. |
DESeq2 v. 1.22.2, adjusted p-value <= 0.05. |
WBPaper00059605:mut-16(pk710)_upregulated
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Transcripts that showed significantly increased expression in npr-15(tm12539) comparing to in N2 at L4 larva stage. |
Fold change > 2, FDR < 0.05. |
WBPaper00066608:npr-15(tm12539)_upregulated
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Transcriptions that showed significantly increased expression in skn-1(RNAi) comparing to empty vector injection into rrf-3(pk1426);daf-2(e1368) animals. |
Genes with an absolute fold changeof at least 2 and standard p-values below 0.05 were considered as differentially expressed. |
WBPaper00062193:skn-1(RNAi)_upregulated
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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 crh-1(syb385) comparing to in N2 animals. |
DESeq2 v1.26.0, FDR < 0.01. Fold change > 2. |
WBPaper00062440:crh-1(syb385)_upregulated
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Transcripts detected in germline isolated from day-1 adult hermaphrodite animals. |
All three experiments have CPM >= 1. |
WBPaper00067147:germline_expressed
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Bacteria: B.thuringiensis |
Transcripts in N2 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_N2
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