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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
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Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology. |
DESEQ2, fold change > 2 and FDR < 0.01. |
WBPaper00062103:neuron_enriched
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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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Up-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_upregulated
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Transcripts down regulated in hpl-2(tm1489) embryo comparing to N2 in tiling array analysis. |
Oligos from the tiling array were mapped to chromosome coordinates of the exons from Wormbase WS180. Any oligo that mapped to a gene on both the Watson and Crick strands was excluded. The remaining oligos were then grouped together (perfect match and mismatch) into probe sets and written out into an Affymetrix CDF file. The CDF file was converted into an R-package and loaded into R. The expression values were calculated using the justRMA function from Bioconductor. This used a Benjamini and Hochberg false discovery rate correction. |
WBPaper00040560:hpl-2_embryo_downregulated
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Bacteria infection: Photorhabdus luminescens |
Genes with increased expression after 24 hours of infection by P.lumniescens 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:P.lumniescens_24hr_upregulated_TilingArray
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Transcripts that showed significantly decreased expression in mex-1(or286) comparing to in N2 at early embryo when there were only 3 -5 eggs in the adult. |
RPKM fold change > 2. |
WBPaper00058598:mex-1(or286)_downregulated
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Transcripts that showed significantly decreased expression in drh-3(rrr2) comparing to in N2. |
edgeR, log2 fold change > 2 or < -2. |
WBPaper00053888:drh-3(rrr2)_downregulated
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Genes that showed significantly increased expression level in rsr-2(RNAi) animals comparing to in gfp(RNAi) control. |
Fold change > 1.2 or < 0.8. |
WBPaper00042477:rsr-2(RNAi)_upregulated_TilingArray
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Transcripts that showed significantly increased expression in sensory neuron (labeled by iaIs25[Pgcy-37::GFP + unc-119(+)]) comparing to in whole worm. |
Fold change > 2, p-value < 0.05. |
WBPaper00060661:sensory-neuron_enriched
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Genes that showed significantly increased expression after exposure to adsorbable organic bromine compounds (AOBr) contained in M. aeruginosa batch culture. |
Differentially expressed genes (DEGs) were identified with a random variance t-test and a significance analysis of microarrays (SAM) test. Genes were considered statistically significant if their p-value was less than 0.05, the false discovery rate less than 0.3, and the fold change compared to control at least <= 0.67 or >=1.5. |
WBPaper00046853:AOBr_M.aeruginosa-batch-culture_upregulated
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Coexpression clique No. 211, srj-42-srw-113, 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:srj-42-srw-113
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Up-regulated genes (fold change > 1.5) rescued by CoQ10 supplementation (80-120 %) 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_upregulated_CoQ10_dependent
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mRNAs that bind with neuronally expressed FLAG-tagged UNC-75 in unc-75(null) mutants CZ14662[unc-75(e950); Prgef-1-UNC-75S(juIs369)], according to CLIP-seq analysis. |
N.A. |
WBPaper00049626:UNC-75_target
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Genes predicted to be upregulated more than 2.0 fold in rde-3(r459) mutant worms as compared to wild-type animals (t-test P-value < 0.05). |
A t-test (5% confidence) was applied to the triplicate sample data for each transcript in each mutant to identify genes significantly elevated or decreased compared with the wild type. |
WBPaper00027111:rde-3(r459)_upregulated
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Genes predicted to be upregulated more than 2.0 fold in rrf-3(pk1426) mutant worms as compared to wild-type animals (t-test P-value < 0.05). |
A t-test (5% confidence) was applied to the triplicate sample data for each transcript in each mutant to identify genes significantly elevated or decreased compared with the wild type. |
WBPaper00027111:rrf-3(pk1426)_upregulated
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Genes predicted to be upregulated more than 2.0 fold in eri-1(mg366) mutant worms as compared to wild-type animals (t-test P-value < 0.05). |
A t-test (5% confidence) was applied to the triplicate sample data for each transcript in each mutant to identify genes significantly elevated or decreased compared with the wild type. |
WBPaper00027111:eri-1(mg366)_upregulated
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Single-cell RNA-Seq cell group 66_0 expressed in neuron. |
scVI 0.6.0 |
WBPaper00065841:66_0
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