Genomics
8 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:B0041.2b.1 | B0041.2b.1 |
3137
 |
I: 4653467-4660153 |
| Transcript:B0041.2f.1 | B0041.2f.1 |
3066
|
I: 4653473-4660148 |
| Transcript:B0041.2a.1 | B0041.2a.1 |
3135
|
I: 4653473-4660151 |
| Transcript:B0041.2e.1 | B0041.2e.1 |
3075
|
I: 4653473-4660151 |
| Transcript:B0041.2d.1 | B0041.2d.1 |
2247
|
I: 4653527-4659317 |
| Transcript:B0041.2c.1 | B0041.2c.1 |
2978
|
I: 4655343-4660153 |
| Transcript:B0041.2g.1 | B0041.2g.1 |
2913
|
I: 4655347-4660146 |
| Transcript:B0041.2a.2 | B0041.2a.2 |
2975
|
I: 4655349-4660150 |
Other
7 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:B0041.2b | B0041.2b |
2241
|
I: 4653527-4653542 |
| CDS:B0041.2e | B0041.2e |
2187
|
I: 4653527-4653542 |
| CDS:B0041.2f | B0041.2f |
2181
|
I: 4653527-4653542 |
| CDS:B0041.2c | B0041.2c |
2115
|
I: 4655370-4655496 |
| CDS:B0041.2g | B0041.2g |
2061
|
I: 4655370-4655496 |
| CDS:B0041.2a | B0041.2a |
2121
|
I: 4655370-4655496 |
| CDS:B0041.2d | B0041.2d |
2247
|
I: 4653527-4653542 |
108 Allele
| Public Name |
|---|
| gk962706 |
| gk963902 |
| gk964159 |
| gk964070 |
| tm11186 |
| WBVar01431444 |
| WBVar01431443 |
| WBVar01431441 |
| gk781135 |
| gk666883 |
| gk886139 |
| gk843779 |
| gk771339 |
| gk890401 |
| gk806896 |
| gk734086 |
| gk843778 |
| gk693413 |
| gk613522 |
| gk359464 |
| gk606126 |
| gk480270 |
| gk827750 |
| gk383837 |
| gk702316 |
| gk726614 |
| gk417413 |
| gk333118 |
| gk606815 |
| gk415897 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00015007 | 4653467 | 4660153 | 1 |
3 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrI_4660154..4660520 | 367 | I: 4660154-4660520 | Caenorhabditis elegans |
124 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells. | DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. | WBPaper00060811:L1_vs_adult_upregulated_neural | |
| Transcripts expressed in neuronal cells, by analyzingfluorescence-activated cell sorted (FACS) neurons. | DESeq. False discovry rate (FDR) < 0.1. | WBPaper00048988:neuron_expressed | |
| 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:all-neurons_L1-larva_expressed | |
| mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis. | Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05. | WBPaper00045420:fertilization_downregulated_transcript | |
| Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rifampicin_upregulated | |
| Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin and 50mM Metformin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rapamycin-Metformin_upregulated | |
| Proteins interacting with NHR-49-GFP according to co-IP and LC-MS. | N.A. | WBPaper00064071:NHR-49_interacting | |
| Transcripts expressed in the epithelial tissues surrounding the pharynx that includes the arcade and intestinal valve (AIV) cells, according to PAT-Seq analysis using Pbath-15-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:arcade_intestinal-valve_expressed | |
| Transcripts expressed in body muscle, according to PAT-Seq analysis using Pmyo-3-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:body-muscle_expressed | |
| Transcripts expressed in GABAergic neuron, according to PAT-Seq analysis using Punc-47-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:GABAergic-neuron_expressed | |
| Transcripts expressed in hypodermis, according to PAT-Seq analysis using Pdpy-7-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:hypodermis_expressed | |
| Transcripts expressed in intestine, according to PAT-Seq analysis using Pges-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:intestine_expressed | |
| Transcripts expressed in NMDA neuron, according to PAT-Seq analysis using Pnmr-1-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:NMDA-neuron_expressed | |
| Transcripts expressed in pharynx, according to PAT-Seq analysis using Pmyo-2-GFP-3XFLAG mRNA tagging. | Cufflinks FPKM value >=1. | WBPaper00050990:pharynx_expressed | |
| Genes with expression level regulated by genotype (N2 vs CB4856) and age 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_age_regulated_developing | |
| 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 |
| Maternal class (M): genes that are called present in at least one of the three PC6 replicates. | A modified Welch F statistic was used for ANOVA. For each gene, regressed error estimates were substituted for observed error estimates. The substitution is justified by the lack of consistency among the most and least variable genes at each time point. Regressed error estimates were abundance-dependent pooled error estimates that represented a median error estimate from a window of genes of similar abundance to the gene of interest. A randomization test was used to compute the probability Pg of the observed F statistic for gene g under the null hypothesis that developmental time had no effect on expression. P-values were not corrected for multiple testing. | [cgc5767]:expression_class_M | |
| 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 | |
| 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 | |
| Genes down regulated by mir-243(n4759). | RNAs that changed at least 2-fold with a probability of p > 0.05 in three biological replicates were considered differentially regulated between wild-type and mir-243. | WBPaper00036130:mir-243_down_regulated | |
| Transcripts detected in body muscle nuclei according to a nuclear FACS-based strategy. | Cufflinks | WBPaper00065120:body-muscle-transcriptome | |
| 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:all-neurons_L2-larva_expressed | |
| Transcripts that showed significantly increased expression in nuo-6(qm200) comparing to in N2. | Differential gene expression analysis was performed using the quasi-likeli-hood framework in edgeR package v. 3.20.1 in R v. 3.4.1. | WBPaper00053810:nuo-6(qm200)_upregulated | |
| 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:coelomocytes_L2-larva_expressed | |
| 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 | |
| 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 | |
| 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 | |
| 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:glr-1(+)-neurons_L2-larva_expressed | |
| 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 | |
| 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:intestine_L2-larva_expressed |
8 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2009273 | Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans). | |||
| Picture: Figure S1. | Expr7851 | The GFP signal was visible in all tissues. | ||
| Expr1036414 | Tiling arrays expression graphs | |||
| Expr13424 | ||||
| Expr2027510 | Single cell embryonic expression. Only cell types with an expression fraction of greater 0.2 of the maximum expressed fraction are labeled (Full data can be downloaded from http://caltech.wormbase.org/pub/wormbase/datasets-published/packer2019/). The colors represent the broad cell class to which the cell type has been assigned. The size of the point is proportional to the log2 of the numbers of cells in the dataset of that cell type. Interactive visualizations are available as a web app (https://cello.shinyapps.io/celegans/) and can also be installed as an R package (https://github.com/qinzhu/VisCello.celegans). | |||
| Expr10993 | AIN-2::GFP is diffusely localized in wild-type embryos. | |||
| Expr1142893 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr1010251 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 |
4 Ontology Annotations
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| involved_in | |
| involved_in | |
| involved_in |
10 Regulates Expr Cluster
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| 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 | |
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|
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
|
| |
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|
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
|
| |
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|
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|
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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miRNA targets that are significantly enriched at L4 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|
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:L4_enriched_AIN-2_IP
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| Genes enriched in neuronal miRNA-induced silencing complexes (miRISC) as detected by immunoprecipitations and microarray analysis. | Testable genes were defined as having reliable signals in two different biological replicates using the Agilent microarray chip. Multiple probes for the same gene were removed, keeping the probe with the lowest p-value as defined by a one-tailed t-test comparing all testable probes versus probes towards a designated gene. The testable data was then supplemented with the enrichment values (as percent ranks) of a fifth replicate, from another microarray platform GPL5883 (which had a single probe for each gene), and statistical significance was re-calculate. p < 0.001 was the final cutoff. | WBPaper00042548:miRISC_enriched | |
| Genes enriched in L4 larva intestinal AIN-2 miRISCs, potentially involved in non-development processes. Pges-1-ain-2-gfp IP was performed in synchronized L4 larva. | Enrichment values are expressed as mean percent rank. The p value was computed by comparing all enrichment values for a given transcript to all enrichment values of all transcripts by a one-tailed t test. Significantly enriched genes are those with p value < 0.01. | WBPaper00040985:AIN-2_L4_intestine | |
| Genes enriched in intestinal AIN-2 miRISCs. Pges-1-ain-2-gfp IP was performed in mixed stage worms. | Enrichment values are expressed as mean percent rank. The p value was computed by comparing all enrichment values for a given transcript to all enrichment values of all transcripts by a one-tailed t test. Significantly enriched genes are those with p value < 0.01. | WBPaper00040985:AIN-2_asynchronous_intestine | |
| Genes enriched in body wall muscle AIN-2 miRISCs. Pmyo-3-ain-2-gfp IP was performed in mixed stage worms. | Enrichment values are expressed as mean percent rank. The p value was computed by comparing all enrichment values for a given transcript to all enrichment values of all transcripts by a one-tailed t test. Significantly enriched genes are those with p value < 0.01. | WBPaper00040985:AIN-2_asynchronous_muscle |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrI_4652907..4653466 | 560 | I: 4652907-4653466 | Caenorhabditis elegans |
