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Genes upregulated in dcr-1(-/-) adult animals by at least 1.5 fold and P < 0.01, as determined by a multisample t-test and the Benjamini and Hochberg false discovery rate correction. |
Statistical t-test: P < 0.05 for rde-4(-/-) and rde-1(-/-) analyses; P < 0.01 for dcr-1(-/-) analysis with a threshold of 1.5-fold misregulation. |
WBPaper00029437:dcr-1_upregulated
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Genes that showed lower expression in N2 than in DR1350. |
The normalised data were analysed using a two-way ANOVA, testing for each gene the effects of LINE (N2, DR1350, RIL-14, RIL-17), TREATMENT (non-dauer vs dauer larva-inducing) and the LINE TREATMENT interaction, using a published PERL script. |
WBPaper00034739:N2lessDR1350
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Genes from N2 animals with significantly increased expression after 72 hours of treatment on growth media with 10uM rapamycin in 2% DMSO. |
Analysis of gene expression data was carried out with the Affymetrix Transcriptome Analysis Console. Data preprocessing (using RMA normalization) and QC metrics were performed using Affymetrix Expression Console TM and manually inspected afterwards. Expression analysis was carried out for each two pairwise conditions. FDR statistical correction for multiple testing resulted in a slightly lower number of DEGs in most cases. P-value < 0.05 and fold change > 2.0 were used to determine differentially expressed genes. |
WBPaper00048989:N2_rapamycin_upregulated
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Genes that showed more than 2 fold decreased expression in oga-1(ok1207) comparing to in N2 when fed with OP50. |
The significantly expressed genes were selected based on ANOVA analysis by Partek Genomics Suite software. Genes with a p-value of <0.05 and a 2-fold or greater fold change were considered differentially expressed. |
WBPaper00046083:oga-1(ok1207)_OP50_downregulated
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Genes that showed more than 2 fold decreased expression in ogt-1(ok1474) comparing to in N2 when fed with OP50. |
The significantly expressed genes were selected based on ANOVA analysis by Partek Genomics Suite software. Genes with a p-value of <0.05 and a 2-fold or greater fold change were considered differentially expressed. |
WBPaper00046083:ogt-1(ok1474)_OP50_downregulated
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mRNAs that were significantly enriched in the AIN-2 immunoprecipitation samples, compared to the control total mRNAs in the input extracts (p < 0.01). |
Signals from replicates of total worm lysates from wt and strains containing the ain-2::gfp or the ain-2 promoter::gfp transgene were mean normalized and averaged respectively to generate standard profiles of gene expression in these worm strains. Authors then calculated the ratio of signal of each gene from each IP sample to the standard gene expression profile of the corresponding worm strain. Based on this ratio, a percentile rank of each gene relative to all genes in each IP replicate was calculated. The percentile ranks in the three replicates of each IP were averaged. Student t test was utilized to determine if the average percentile ranks of enrichment of individual genes were significantly higher (p value) than the mean enrichment of all genes in the IP samples. To determine the AIN-1 or AIN-2 associated genes, we used the following criteria: (1) average percentile ranks of enrichment is greater than the mean enrichment of all genes in AIN-1 or AIN-2 IP with p < 0.01; (2) average signal in AIN-1 or AIN-2 IP replicates is greater than the background signal (including 2X standard deviation (SD)) (Background signal and SD were calculated based on signals from empty spots on each microarray); (3) criteria 1 is not be satisfied for the same gene in the corresponding control IP. |
WBPaper00031252:AIN-2_IP_enriched
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miRNA targets that are significantly enriched at embryo 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:embryo_enriched_AIN-2_IP
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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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miRNA targets that are significantly enriched at L2 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:L2_enriched_AIN-2_IP
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miRNA targets that are significantly enriched at L3 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:L3_enriched_AIN-2_IP
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Genes that showed more than 1.5-fold increase of expression following (Pore-Forming Toxin) PFT treatment by Cry5B. |
Linear Models for Microarray Data (LIMMA) was used to determine a set differentially expressed genes. The cutoff p-value used was 0.01 with minimum 1.5 or 2 fold change. |
WBPaper00038231:Cry5B_1.5-fold_upregulated
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Genes that showed more than 2-fold increase of expression following (Pore-Forming Toxin) PFT treatment by Cry5B. |
Linear Models for Microarray Data (LIMMA) was used to determine a set differentially expressed genes. The cutoff p-value used was 0.01 with minimum 1.5 or 2 fold change. |
WBPaper00038231:Cry5B_2-fold_upregulated
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