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Heat shock: 35C for 1 hour. |
Transcripts that showed significantly increased expression immediately after 1-day post L4 adult hermaphrodite N2 animals were exposed to 35C for 1 hour. |
The DESeq2 (GalaxyVersion 2.11.40.6 + galaxy1) was used to determine differentiallyexpressed features from count tables of differential transcript abundances. log2FC > 1, FDR < 0.01. |
WBPaper00065749:Heat-Shock_upregulated_N2
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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 that showed significantly decreased expression in daf-16(mgDf50) comparing to in N2 at L1 larva stage. |
DESeq v1.20.0 was used to analyze differential gene expression. Transcripts with adjusted p-value < 0.05 were considered differentialled expressed. |
WBPaper00048971:daf-16(mgDf50)_downregulated_L1
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Genes that were not enriched in either spermatogenic fem-3(q96gf) nor oogenic fog-2(q71) gonads, according to RNAseq analysis. |
To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. |
WBPaper00045521:Gender_Neutral
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Transcripts that showed significantly decreased expression in sek-1(km4) animals comparing to in N2 animals under both dietary (DR, OP50 OD = 0.1) and ad libtum (AL, OP50 OD = 3) conditions from 3-day post L4 till 6-day post L4 adult hermaphrodite stage. |
Bioconductor package edgeR, p < 0.05. |
WBPaper00056443:sek-1(km4)_downregulated
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Genes with differential expression under 0.5mg/l Chlorpyrifos (CPF) and 0.5mg/l Diazinon (DZN) treatment at 24 centigrade. |
To identify the differentially expressed genes in each treatment authors used linear models per toxicant and temperature (gene expression = Toxicant (effect) + error). The lm function in R stats package was used to implement the linear models analysis with recommended default options. For threshold determination authors used a permutation approach. For each of the 23,232 permutations used authors randomly picked a transcript (array spot), which could only be picked once. Authors combined all the expression values of this transcript and randomly distributed them over the replicates and used them in the linear model. In this way authors obtained a threshold for each of the toxicants. Authors used a -log10 p-value 2 as common threshold for the analysis, which resembles to the following FDR per toxicant: 0.0155 for CPF at 24 centigrade, 0.0148 for DZN at 24 centigrade, 0.0168 for CPF+DZN at 24 centigrade, 0.0142 for CPF at 16 centigrade, 0.0151 for DZN at 16 centigrade, and 0.0148 for CPF+DZN, at 16 centigrade. |
WBPaper00040210:Chlorpyrifos_Diazinon_24C_regulated
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Transcripts that showed significantly increased expression in hsf-1(RNAi) animals comparing to in control 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:hsf-1(RNAi)_upregulated
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Transcripts that showed significantly increased expression in csr-1(RNAi) comparing to in N2 animals fed wth empty vector. |
DESeq2 v1.20.0,, fold change > 2, FDR < 0.05. |
WBPaper00066919:csr-1(RNAi)_upregulated
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Transcripts that showed significantly increased expression in animals with pan-neuronal expression of human amyloid beta (snb-1p-Amyloid-beta(1-42) + mtl-2p-GFP), comparing to in N2 animals. |
edgeR p-value < 0.01 and fold change > 4. |
WBPaper00061613:human-amyloid-beta_upregulated
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miRNA targets that are significantly enriched at L1 larva stage. To generate a global view of the dynamics of miRNA-mediated regulation of gene expression during C. elegans development, authors analyzed the mRNAs in the AIN-2-GFP IP results from five developmental stages. The magnitude of the combined interaction of miRNAs with a given target mRNA was assessed by measuring the fold enrichment of that mRNA in AIN-2 IP samples, relative to the abundance of the mRNA in the corresponding total lysate. Because this enrichment in the IP sample versus total lysate directly reflects the miRISC-associated fraction of a given mRNA, high enrichment indicates the likelihood of strong miRNA-mediated regulation of the mRNA, whereas low or negative enrichment indicates the likelihood of weak or absent miRNA regulation of the mRNA. It is also possible that poor enrichment could reflect interactions that occur only in a rare subset of cells at any given stage of development. Transcripts that were significantly enriched (0
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For each transcript represented on the microarray, authors first used all 18 data points from all of the 18 microarrays to calculate its average in-stage standard deviation as SD=SQRT((i=1-K (ni-1)SDi2)/(N-K)), degree of freedom (df)=N-K, where K is the number of developmental stages in which the given transcript had at least one non-missing log2(IP/Total) value; ni is the number of non-missing values in stage i among the K stages; SDi is the standard deviation of the log2(IP/Total) values from all the replicates of stage i; N is the total number of non-missing values for this transcript at all stages. A transcript must have at least one stage with at least two non-missing values to be testable. All of the non-missing values of a transcript at each stage were averaged to generate the stage-average values (Mi for stage i). The standard error of Mi was calculated as SEi=SD/SQRT(ni) (df=N-K), where SD is the average in-stage standard deviation calculated above and ni is the number of non-missing values at stage i, as explained above. Based on the SEi, a one-tailed Students t-test was used to calculate the P-value of enrichment in stage i (Test if Mi>0). The T statistic was constructed as T=Mi/SEi (df=N-K). Mi>0 and enrichment P<0.001 were used as the threshold of enrichment for each stage. |
WBPaper00035084:L1_enriched_AIN-2_IP
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Transcripts that showed significantly decreased 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:downregulated_P-granule(-)GFP(+)_vs_control_day2-adult
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Transcripts that showed significantly increased expression in mrpl-2(osa3) comparing to wild-type animals. |
Differential expression analysis was performed using DESeq2R package(v.1.10.1).Relative expression of genes with Benjamini-Hochberg corrected P-values (Padj)<0.05 were considered to be differentially expressed. |
WBPaper00060951:mrpl-2(osa3)_upregulated
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