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Transcripts of coding genes that showed significantly decreased 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_depleted_coding-RNA
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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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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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Bacteria infection: Bacillus thuringiensis |
mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 10 mix) vs BT407 12h), according to RNAseq. |
Cuffdiff, ajusted p-value < 0.01. |
WBPaper00046497:B.thuringiensis_0.1mix_downregulated_12h
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Bacteria infection: Bacillus thuringiensis |
mRNAs that showed significantly decreased expression after pathogenic bacteria Bacillus thuringiensis infections comparing to non pathogenic BT (BT247(1 to 2 mix) vs BT407 12h), according to RNAseq. |
Cuffdiff, ajusted p-value < 0.01. |
WBPaper00046497:B.thuringiensis_0.5mix_downregulated_12h
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Transcripts that showed significantly changed expression in 6-day post-L4 adult hermaphrodite comparing to in 1-day post L4 adult hermaphrodite animals. |
Sleuth |
WBPaper00051558:aging_regulated
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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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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
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Gamma irradiation 100 mGY per hour for 72 hours since L1 larva. |
Transcripts that showed significantly increased expression after exposure to 100mGy per hour gamma irradiation from L1 to day 1 adult hermaphrodite stage. |
DESeq2, FDR <= 0.05, log2 fold change >= 0.3 or <= -0.3. |
WBPaper00058958:100mGy-irradiation-72h_upregulated
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Transcripts that showed significantly decreased expression in tetraploid N2 comparing to diploid N2 animals at L4 larva stage. |
DESeq2 R package (1.20.0), fold change > 2, and FDR < 0.05. |
WBPaper00066110:tetraploid_vs_diploid_downregulated
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Genes that showed expression levels higher than the corresponding reference sample (L3/L4 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:dopaminergic-neurons_L3-L4-larva_expressed
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Transcripts that showed significantly increased 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)_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 increased expression in hda-1(RNAi) embryos comparing to control animals. |
DESeq2, fold change > 2, FDR < 0.05. |
WBPaper00067044:hda-1(RNAi)_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 elt-2(RNAi) 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_elt-2(RNAi)
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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 decreased expression in the neurons of bcat-1(RNAi) animals at 5-days post L4 adult hermaphrodite stage, comparing to animals injected with empty vector. |
DESeq2. FDR < 0.05. |
WBPaper00060459:bcat-1(RNAi)_downregulated
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Transcripts that showed significantly decreased expression in nhl-2(ok818) comparing to in N2 at 25C. |
EdgeR, FDR < 0.05, fold change < 0.5. |
WBPaper00055971:nhl-2(ok818)_25C_upregulated
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Transcripts that showed significantly increased expression in animals lacking P granules by RNAi experiments targeting pgl-1, pgl-3, glh-1 and glh-4, and unc-119-GFP(+), comparing to in control animals, at 2-day post L4 adult hermaphrodite stage. |
DESeq2, Benjamini-Hochberg multiple hypothesis corrected p-value < 0.05 and fold change > 2. |
WBPaper00050859:upregulated_P-granule(-)GFP(+)_vs_control_day2-adult
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TGF- Dauer pathway adult transcriptional targets. Results obtained by comparing the microarray results of the dauer-constitutive mutants daf-7(e1372), daf-7(m62), and daf-1(m40) with dauer-defective mutants daf-3(mgDf90), daf-5(e1386), and daf-7(e1372);daf-3(mgDf90) double mutants at the permissive temperature, 20C, on the first day of adulthood. |
SAM |
WBPaper00031040:TGF-beta_adult_downregulated
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Dietary restriction |
Transcripts that showed significantly increased expression after N2 animals were under dietary restriction (DR, OP50 OD = 0.1) from 3-day post L4 till 6-day post L4 adult hermaphrodite stage, comparing to under ad libtum (AL, OP50 OD = 3) condition. |
Bioconductor package edgeR, p < 0.05. |
WBPaper00056443:DietaryRestriction_upregulated
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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:intestine_L1-larva_expressed
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Transcripts that showed significantly decreased expression in whole animal day 1 N2 adults comparing to in whole animal day 8 N2 adults. |
DESeq2, FDR < 0.05, fold change > 2. |
WBPaper00066978:Day1Adult_vs_Day8Adult_downregulated_neuron
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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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Transcripts that showed significantly increased expression in xpf-1(tm2842) comparing to in N2 animals. |
DESeq2 1.14.1, fold change > 2, FDR < 0.01. |
WBPaper00062497:xpf-1(tm2842)_upregulated
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Bacteria diet: complex environmental microbiotas |
Transcripts that showed significantly decreased expression after L1 larva grew on soil microbiota at 25C for 3 days. |
N.A. |
WBPaper00056139:soil-microbiota_downregulated
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