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Transcripts that showed significantly higher expression in somatic gonad precursor cells (SGP) vs. head mesodermal cells (hmc). |
DESeq2, fold change >= 2, FDR <= 0.01. |
WBPaper00056826:SGP_biased
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Bacteria infection: Enterococcus faecalis OG1RF. Exposure for 16 hours. |
Transcripts that showed significantly decreased expression in N2 after animals were exposed to E. faecalis OG1RF for 16 hours comparing to exposure to E. Coli OP50. |
Cuffcompare and Cuffdiff |
WBPaper00056090:E.faecalis_downregulated_N2
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Transcripts depleted in purified oocyte P bodies comparing to in whole oocytes. |
DESeq2, FDR < 0.05, fold change > 2. |
WBPaper00065975:P-body_vs_oocyte_depleted
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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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Transcripts that showed significantly decreased expression in hpl-2(tm1489) comparing to in N2 animals. |
DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2. |
WBPaper00054493:hpl-2(tm1489)_downregulated
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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 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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Transcripts that showed significantly increased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals. |
DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. |
WBPaper00060014:set-2(tm1630)_upregulated
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Transcripts that showed significantly increased expression in sftb-1(cer6) deletion homozygous comparing to to in N2 animals at L4 larva stage. |
DESeq2, fold change > 2 |
WBPaper00058725:sftb-1(cer6)_upregulated
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Transcripts enriched in germline by comparing dissected germline tissue with dissected intestine tissue, both injected with empty RNAi vector. |
Genes were determined germline-enriched if the lowest expression value (log2(FPKM+1)) observed in the germline empty vector samples was at least 2-fold higher than the highest expression value observed in the intestine empty vector samples. |
WBPaper00051039:germline_enriched
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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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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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Genes that showed significantly decreased expression after exposure to 1mg/L MWCNTs from L1 larva to young adult. |
Transcripts with false discovery rate-corrected p-values < 0.05 and fold change > 2 were defined as differentially expressed. |
WBPaper00049377:MWCNT_downregulated
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Transcripts that showed significantly decreased 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_downregulated_neural
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Transcripts that showed significantly decreased expression in mrps-5(RNAi) animals comparing to animals injected with empty vector. |
Differential expression was assessed using a Partial least-squares discriminant analysis (PLS-DA) using mixomics setting a variable of importance (VIP) score of greater than 1 as significant. |
WBPaper00059328:mrps-5(RNAi)_downregulated_mRNA
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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
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Transcripts of noncoding 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_noncoding-RNA
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Transcripts that showed significantly increased expression in strain CER276 sftb1(cer39[Q552P, R643C,K718E]) comparing to in N2 animals at L4 larva stage. |
DESeq2, fold change > 2 |
WBPaper00058725:sftb-1(cer39)_upregulated
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Protein coding genes with decreased expression in prg-1(wm161) comparing to in N2. |
Cuffdiff and DEGseq were used to calculate the differential expression of protein-coding genes with and without the prg-1 mutation, and authors selected genes which had more than two-fold difference in expression (P < 0.05, q < 0.01 of Storey) from DEGseq outcomes. The intersection of genes which authors selected from DEGseq outcomes and genes which had more than two-fold difference in expression (P < 0.05) from Cuffdiff outcomes was defined as differentially expressed genes. |
WBPaper00045316:prg-1_downregulated_L4
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Genes with small RNAs upregulated in all four meg-3(ax3055) meg-4(ax3052) strains comparing to N2 |
DESeq2 |
WBPaper00057162:meg-3_meg-4_upregulated_sRNA
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ncRNAs with significantly decreased expression in cep-1(gk138) than in N2 after UV irradiation, according to RNAseq. |
ncRNAs with more than 2 fold difference in expression are considered differentially expressed |
WBPaper00045380:cep-1(gk138)_downregulated_UV
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Transcripts that showed significantly decreased expression in animals overexpression human amylin (driven by hsp-16.2). |
Differential gene expression analysiswas conducted using the DESeq R package (available from Bio-conductor). The DESeq analysis resulted in the determination of potential differentially expressed genes when compared between the DMH46 and N2 (wildtype) samples. The read counts for each sample were normalized for sequencing depth and distortion caused by highly differentially expressed genes.Then the negative bi nomial (NB) model was used to test the significance of differential expression between two genotypes.The differentially expressed genes were deemed significant if the FDR (False Discovery Rate) was less than 0.05, and the gene expression was above the 10th percentile, and showed greater than 2-fold change difference(overexpressed or underexpressed) between the conditions. |
WBPaper00056731:human-amylin_downregulated
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Genes with < 0.67 fold decreased expression in skn-1(RNAi) animals comparing to in N2 control at 25 centigrade. Fold change = glp-1(ts) + skn-1 RNAi vs. glp-1(ts) + vector |
Fold change > 4.0 for glp-1(ts) regulated genes, and fold change < 0.67 for skn-1(RNAi) regulated genes. |
WBPaper00047132:skn-1(RNAi)_downregulated_glp-1(ts)-dependent
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Transcripts that showed significantly decreased expression in ints-8(RNAi) comparing to in N2. |
DESeq2 and edgeR. |
WBPaper00056284:ints-8(RNAi)_downregulated
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Bacteria: P. aeruginosa infected parents. |
Transcripts that showed significantly decreased expression in embryos from parents fed with P. aeruginosa PA14. |
DESeq2, Fold Change > 2 or < 0.5. |
WBPaper00059566:P.aeruginosa_downregulated
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