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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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Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00066485:ogt-1(ok1474)_upregulated_neuron
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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 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 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 ints-5(RNAi) comparing to in N2. |
DESeq2 and edgeR. |
WBPaper00056284:ints-5(RNAi)_upregulated
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Significantly up-regulated genes (>= 1.5-fold change, q value < 0.05) in blmp-1(tm548) mutant versus N2 L3 larvae as obtained from RNA sequencing analysis (n = 3). |
Differential gene expression was performed with cuffdiff - which is part of the cufflinks package (v2.0.2) Genes with a FPKM value >0.5 in at least one of the N2 and blmp1 samples were considered expressed. Those with a q-value < 0.05 and fold change > +/- 1.5 were classified as differentially expressed. |
WBPaper00045017:blmp-1(tm548)_upregulated
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Transcripts that did not alter expression in smg-1(r910) and smg-1(r910) smg-2(r915) mutants comparing to in N2, but their mRNAs co-purify with SMG-2. |
edgeR |
WBPaper00053308:SMG-2_associated_NMD(-)_unaltered_ClassII
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Down-regulated genes (fold change > 1.5) in two CoQ-deficient clk-1 mutant strains (e2519, qm30) compared to wild types N2. |
Fold-changes of intensities were calculated from the arithmetic mean of gene expression values between experimental and corresponding control group. Fold change >= 1.5 was used as cut-off. |
WBPaper00045774:clk-1_downregulated
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Transcripts that interact with 3xFLAG-DLC-1 as identified by immunoprecipitation followed by RNA sequencing. |
DESeq2, fold change > 2,, p-value < 0.01 |
WBPaper00055334:DLC-1_interacting
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Coexpression clique No. 130, acy-2-F35C5.11, 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:acy-2-F35C5.11
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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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Genes that were enriched in spermatogenic fem-3(q96gf) gonads comparing to in oogenic fog-2(q71), according to RNAseq analysis. |
To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. |
WBPaper00045521:Spermatogenic
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Transcripts that showed significantly decreased expression in numr-1/2(RNAi) animals treated with 300uM CdCl2 from L1 to late L3 larva stage, comparing to control RNAi animals with the same Cadmium treatment. |
DESeq2, v1.12.0, fold change > 2, FDR < 0.05 |
WBPaper00057068:numr-1(RNAi)_downregulated_Cadmium
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Transcripts that showed significantly increased expression in hira-1(gk835598) comparing to in N2 animals at adult stage. |
Differential expression analysis was done with Rversion 2.15.3 using DESeq_1.10.1. Fold change > 2, p-value < 0.01. |
WBPaper00059739:hira-1(gk835598)_upregulated_adult
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heat shock: 33C 30min |
Transcripts that showed significantly increased expression in hsf-1(RNAi) animals, after heat shock at 33 C for 30min, comparing to in hsf-1(RNAi) animals without heat shock. |
Transcripts that were differentially expressed in different conditions, compared to the hsf-1(+);-HS control, were determined with CuffDiff, which uses the Benjamini-Hochberg correction for multiple testing to obtain the q-value (the FDR-adjusted the p-value). |
WBPaper00049942:HeatShock_upregulated_hsf-1(RNAi)
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Coexpression clique No. 146, nhr-107_19485-nhr-109_3743, 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:nhr-107_19485-nhr-109_3743
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Transcripts that showed significantly increased expression in hira-1(gk835598) comparing to in N2 animals at L1 larva stage. |
Differential expression analysis was done with Rversion 2.15.3 using DESeq_1.10.1. Fold change > 2, p-value < 0.01. |
WBPaper00059739:hira-1(gk835598)_upregulated_L1
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