|
Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. |
DESeq. False discovry rate (FDR) < 0.1. |
WBPaper00048988:neuron_expressed
|
adult vs dauer larva |
Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C. |
N.A. |
WBPaper00050488:adult_vs_dauer_regulated_N2_20C
|
|
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
|
|
Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging. |
Cufflinks FPKM value >=1. |
WBPaper00050990:arcade_intestinal-valve_expressed
|
|
Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging. |
Cufflinks FPKM value >=1. |
WBPaper00050990:hypodermis_expressed
|
|
Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. |
Cufflinks FPKM value >=1. |
WBPaper00050990:intestine_expressed
|
|
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
|
|
Transcripts expressed in vulva. |
FPKM >= 1. |
WBPaper00064122:vulva_transcriptome
|
|
Transcripts that showed significantly increased expression in sin-3(tm1276) comparing to in N2. |
DESeq2, fold change > 2, p-value < 0.01. |
WBPaper00061203:sin-3(tm1276)_upregulated
|
|
Transcripts that showed significantly decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage. |
DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed. |
WBPaper00048971:daf-16(mgDf50)_downregulated_L1
|
|
Transcripts that showed significantly decreased expression in sin-3(tm1276) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. |
DESeq2, fold change > 2, adjusted p-value < 0.01 |
WBPaper00058598:sin-3(tm1276)_downregulated
|
|
Transcripts that showed significantly increased expression in oocyte germline cells comparing to in mitosis germline cells. |
Log2 Fold change > 2 or <-1, p-value < 0.05. |
WBPaper00053599:oocyte_vs_mitosis_upregulated
|
|
Genes with increased RNA expression after 24 hours rotenone treatment |
EdgeR provides 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 Hochbergs approach for controlling the false discovery rate (FDR). Transcripts with an adjusted p-value smaller 0.05 were assigned as differentially expressed. |
WBPaper00044426:rotenone_24h_upregulated
|
|
Transcripts that showed significantly increased expression in flr-1(RNAi) comparing to in control RNAi animals. This is an incomplete list. |
N.A. |
WBPaper00055060:flr-1(RNAi)_downregulated
|
|
Transcripts that showed significantly increased expression in pry-1(mu38) animals comparing to in N2 at L1 larva stage. |
DESeq, FDR < 0.05 |
WBPaper00055626:pry-1(mu38)_upregulated
|
|
Genes that showed decreased expression in wdr-5(ok1417) comparing with in N2. |
Statistical analysis for misexpression was performed using a moderated t test from the package limma. All genes with a false discovery rate (FDR) of <= 5% (p <= 0.05) were selected as differentially regulated. |
WBPaper00045861:wdr-5(ok1417)_downregulated
|
|
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
|
|
Transcripts that showed significantly increased expression in spr-1(ok2144) comparing to in N2. |
DESeq2, fold change > 2, p-value < 0.01. |
WBPaper00061203:spr-1(ok2144)_upregulated
|
|
Transcripts that showed significantly increased expression in emb-4(hc60) comparing to in N2. |
DESeq2 |
WBPaper00052884:emb-4(hc60)_upregulated
|
|
Genes that showed expression levels higher than the corresponding reference sample (Young adult all cell reference). |
A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. |
WBPaper00037950:CEP-sheath-cells_Day1-adult_expressed
|
|
Genes that showed expression levels higher than the corresponding reference sample (embryonic 24hr reference). |
A Mann-Whitney U test with an empirical background model and FDR correction for multiple testing was used to detect expressed transcripts (Benjamini and Hochberg 1995). Genes and TARs with an FDR <= 0.05 were reported as expressed above background. Authors detected differentially expressed transcripts using a method based on linear models. Genes and TARs were called differentially expressed if the FDR was <= 0.05 and the fold change (FC) >= 2.0. To more strictly correct for potential false-positives resulting from multiple sample comparisons, authors divided individual FDR estimates by the number of samplesor sample comparisons, respectively. This resulted in an adjusted FDR of 1.3 * 0.0001 for expression above background and of 7.4 * 0.0001 for differential expression. Authors called genes selectively enriched in a given tissue if they met the following requirements: (1) enriched expression in a given tissue (FDR <= 0.05 and FC >= 2.0), (2) fold change versus reference among the upper 40% of the positive FC range observed for this gene across all tissues, and (3) fold-change entropy among the lower 40% of the distribution observed for all genes. |
WBPaper00037950:dopaminergic-neurons_L1-larva_expressed
|
|
Genes found to be regulated in daf-16(mgDf50) by resveratrol treatment with p < 0.01. |
N.A. |
WBPaper00026929:Resveratrol_regulated_daf-16
|
|
Transcripts that showed significantly decreased expression in jmjd-3.1p::jmjd-3.1 comparing to in N2. |
DESeq2 Benjamini-Hochberg adjusted p-value < 0.05. |
WBPaper00049545:jmjd-3.1(+)_downregulated
|
Temperature Shift: 25C vs 15C for 16 hours at L4 larva stage. |
Transcripts that showed significantly increased expression in AFD neurons comparing to in whole animals. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00065158:AFD_enriched
|
0.5% glucose supplemented OP50 diet. |
Transcripts that showed significantly increased expression in hyl-2(tm2031) fed with glucose diet, comparing to in hyl-2(tm2031) when fed with OP50 only diet. |
Cufflinks was used to identify the genes in glucose-fed C. elegans with significant alteration in their expressions compared to wild-type C. elegans. The transcripts passing the significance test [False discovery rate (FDR) adjusted P-value to be < 0.05] were examined further for their abundance fold change between the conditions. |
WBPaper00049920:Glucose-Diet_upregulated_hyl-2(tm2031)
|
|
Transcripts that showed significantly decreased expression in animals after 24 hour exposure to 100ug per ml silica nanoparticles (SiNPs). |
The random variance model (RVM)t-test was applied toidentify differentially expressed mRNAs and miRNAsbetween the SiNPs-treated group and the control group. P-value <0.05 and fold change (FC) >1.5 were considered as the threshold screening between the SiNP-treated groupand the control group. |
WBPaper00060100:SiNP_downregulated_mRNA
|
|
Transcripts that showed significantly decreased expression in sur-5p::jmjd-1.2 comparing to in N2. |
DESeq2 Benjamini-Hochberg adjusted p-value < 0.05. |
WBPaper00049545:sur-5p-jmjd-1.2(+)_downregulated
|
|
Transcripts that showed significantly decreased expression in pmt-2(RNAi) animals comparing to control animals iinjected with empty vector. |
Fold-change > 1.5, ANOVA P values < 0.05. |
WBPaper00055482:pmt-2(RNAi)_downregulated
|
|
Targets of endo-siRNA that showed significantly increased expression in BFF40[meg-3(tm4259);meg-4(ax2026);mex-5::gfp::h2b::tbb-2] 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:meg-3(tm4259)_meg-4(ax2026)_upregulated
|
|
Transcripts that showed differential expression in adult mir-34(gk437) vs adult mir-34(OverExpression) animals at 20C. |
N.A. |
WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_adult_20C
|