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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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Transcripts that showed significantly increased expression glp-1(e2141); TU3401 animals comparing to in TU3401 animals. |
Fold change > 2, FDR < 0.01. |
WBPaper00065993:glp-1(e2141)_upregulated
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Genes that were downregulated in lin-15B(n744). |
For each gene in each microarray hybridization experiment, the ratio of RNA levels from the two samples was transformed into a log2 value and the mean log2 ratio was calculated. The log2 ratios were normalized by print-tip Loess normalization (Dudoit and Yang, 2002). All genes with a false discovery rate of <= 5% (q <= 0.05) (Storey and Tibshirani, 2003) and a mean fold-change ratio of >= 1.5 were selected for further analysis. |
WBPaper00038168:lin-15B(n744)_downregulated
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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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Transcripts that showed significantly decreased expression in atfs-1(cmh15) (null allele) animals comparing to in N2 animals at L4 larva stage. |
edgeR, fold change > 2, FDR < 0.05 |
WBPaper00060909:atfs-1(cmh15)_downregulated
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Genes with expression level regulated by genotype (N2 vs CB4856) at L3 larva and Late reproduction stage (96 hours at 24 centigrade). |
For model 2, authors used 100 permutations to estimate the FDR threshold. Per permutation, genotypes and ages were independently randomly distributed, keeping the among-gene structure intact. Then for each spot (23,232) on the array, model 2 was tested. The obtained P-values were used to estimate a threshold for each of the explanatory factors. Authors also used a genome-wide threshold of -log10 P-value = 2, which resembles an FDR of 0.072 and 0.060 for marker and the interaction age-marker for the developing worms and FDR of 0.050 and 0.065 for marker and age-marker for the aging worms. For the physiological age effect, authors used a log10 P-value = 8 in developing worms (0.012 FDR) and -log10 P-value = 6 (0.032 FDR). |
WBPaper00040858:eQTL_regulated_developing
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Transcripts that showed significantly decreased expression in day 3 adult hermaphrodite comparing to in L4 larva daf-16(mu86);glp-1(e2141) animals. |
Fold change > 2, FDR < 0.05 |
WBPaper00064088:Day-3-adult_vs_L4_downregulated_daf-16(mu86);glp-1(e2141)
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Bacteria infection: Photorhabdus luminescens |
Genes down-regulated in animals infected with Photorhabdus luminescens compared to the E. coli OP50 control after 24h of infection. |
MAANOVA and BRB-Array-Tools. |
WBPaper00030985:Photorhabdus_luminescens_downregulated
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Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage. |
DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. |
WBPaper00056169:rrf-3(pk1426)_upregulated_embryo
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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
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Transcripts that showed significantly increased expression in aak-1(tm1944);aak-2(ok524) animals comparing to in N2. |
DEseq 1.18.0, adjusted p-value < 0.05. |
WBPaper00056471:aak-1(tm1944);aak-2(ok524)_upregulated
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Transcripts that showed significantly increased expression in alg-1(gk214), comparing to in N2. |
DESeq2, Fold change > 1.5. |
WBPaper00051404:alg-1(gk214)_upregulated
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Transcripts that showed significantly decreased expression in N2 animals exposed to 0.1mM Paraquat from hatching to reaching adult stage. |
DESeq2 version 1.22.2, p < 0.05 |
WBPaper00064716:paraquat_downregulated
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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
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Transcripts that showed significantly increased expression in cco-1(RNAi) comparing to in vector control animals. |
The limma package47 was used for differential expression. Genes with a Benjamini-Hochberg adjusted P-value <0.05 and an absolute log fold change of 2 were considered differentially expressed. |
WBPaper00053402:cco-1(RNAi)_upregulated
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Transcripts that showed significantly increased expression in xrep-4(lax137). |
DESeq2. Genes were selected if their p value < 0.01. |
WBPaper00066062:xrep-4(lax137)_upregulated
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Reduced humidity (98% relative humidity). |
Genes that were down-regulated after one day exposure to reduced humidity (98% relative humidity) according to microarray analysis. |
Multiple hypothesis testing with the Benjamini-Hochberg correction was applied on calculated p-values. A change in the expression level was considered to be significant if the adjusted p-value was less than 0.001. |
WBPaper00044578:reduced-humidity_downregulated_microarray
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Transcripts that showed significantly increased expression in animals with germline-specific inx-14(RNAi) comparing to in aniamls fed with control vector, both exposed to PA14 infection. |
DESeq2. Differentially-expressed genes (DEG) were identified based on two criteria: FDR (False discovery rateusing Benjamini-Hochberg adjusted p-values) < 0.01 and absolute value of log2(Fold Change) > 1. |
WBPaper00066146:germline-inx-14(RNAi)_upregulated_PA14
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Genes that showed oscillating mRNA expression level throughout the 16 hour time courses from L3 larva to young adult. |
The following three lines of R code were used to perform the classification: increasing <-2*amplitude-PC1 < -1.7; oscillating <-!increasing & (amplitude > 0.55); flat <-!increasing & !oscillating; Note that the amplitude of a sinusoidal wave corresponds to only half the fold change between trough and peak. |
WBPaper00044736:oscillating_dev_expression
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Genes down-regulated following nhr-25(RNAi). |
Pair-wise significance testing (mutant/RNAi vs. wild-type/vector) was performed using the Bioconductor package limma and p-values were initially corrected for multiple testing using the false discovery rate (FDR) method of Benjamini and Hochberg. Authors defined differential expression as log2(ratio) >= 0.848 with the FDR set to 5%, and p-value <= 0.001. |
WBPaper00045015:nhr-25(RNAi)_downregulated
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Genes that showed expression levels higher than the corresponding reference sample (L2 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:excretory-cell_L2-larva_expressed
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Genes that showed expression levels higher than the corresponding reference sample (L2 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:GABAergic-motor-neurons_L2-larva_expressed
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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:hypodermis_L3-L4-larva_expressed
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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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Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals. |
DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2. |
WBPaper00062159:hda-2(ok1479)_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 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Psora-Allantoin_downregulated
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Transcripts that showed significantly decreased expression after animals were treated with 100uM Rapamycin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. |
DESeq2(v1.14.1), fold change > 2, p-value < 0.05 |
WBPaper00055354:Rapamycin-Allantoin_downregulated
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Transcripts that showed significantly increased expression in dpy-21(e428) comparing to in N2 during L3 stage. |
DESeq v1.6.3. Fold change > 1.5. |
WBPaper00050370:dpy-21(e428)_L3_upregulated
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