Genomics
2 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:T09A5.13b | T09A5.13b |
22
 |
II: 7850522-7850543 |
| Transcript:T09A5.13a | T09A5.13a |
24
|
II: 7850559-7850582 |
Other
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00003285 | 7850499 | 7850597 | -1 |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrII_7849798..7850498 | 701 | II: 7849798-7850498 | Caenorhabditis elegans |
22 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Bacteria infection: Pseudomonas aeruginosa PA14. 24 hours of exposure. | Small RNAs (21-26nt) that showed significantly increased expression after L4 animals were exposed to P .aeruginosa strain PA14 for 24 hours. | DESeq2, FDR < 0.05 | WBPaper00056868:P.aeruginosa_upregulated_smallRNA |
| Genes with small RNAs upregulated in all four meg-3(ax3055) meg-4(ax3052) strains comparing to N2 | DESeq2 | WBPaper00057162:meg-3_meg-4_upregulated_sRNA | |
| Micro RNAs that showed significantly decreased expression in day 8 adults comparing to in day 1 adults in intestine. | Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2. | WBPaper00066447:Day8_vs_Day1_downregulated_intestine | |
| Micro RNAs that showed significantly decreased expression in day 8 adults comparing to in day 1 adults in coelomocyte. | Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2. | WBPaper00066447:Day8_vs_Day1_downregulated_coelomocyte | |
| Micro RNAs that showed significantly increased expression in hrpk-1(tm5522) comparing to in N2 at L4 larva stage. | DESeq, fold change > 2, p-value <= 0.05. | WBPaper00058673:hrpk-1(tm5522)_upregulated_miRNA_L4 | |
| MicroRNAs that showed significantly decreased expression in alg-5(ram2), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-5(ram2)_downregulated_miRNA | |
| MicroRNAs that showed significantly decreased expression in alg-1(gk214), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-1(gk214)_downregulated_miRNA | |
| MicroRNAs that showed significantly decreased expression in alg-2(ok304), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-2(ok304)_downregulated_miRNA | |
| MicroRNAs that showed significantly increased expression in alg-2(ok304), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-2(ok304)_upregulated_miRNA | |
| MicroRNAs that showed significantly decreased expression in alg-5(tm1163), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-5(tm1163)_downregulated_miRNA | |
| MicroRNAs that showed significantly decreased expression in Day 5 (5-days post-L4) vs. Day 0 (L4 larva) of adulthood N2 animals. | Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method. | WBPaper00053318:Aging_downregulated_miRNA_N2 | |
| miRNAs that showed significantly decreased expression after 48 hour treatment in 10uM sanguinarine. | Fold change > 2. | WBPaper00055663:sanguinarine_downregulated | |
| MicroRNAs that showed significantly increased expression in alg-5(ram2), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-5(ram2)_upregulated_miRNA | |
| MicroRNAs that showed significantly increased expression in mir-71(n4115) comparing to in N2 at 4-days post L4 adult hermaphrodite. | Differential expression for both small RNA- and mRNA-seq data was tested using DESeq2; P-values were adjusted for multiple testing by Benjamini-Hochberg method. | WBPaper00053318:mir-71(n4115)_upregulated_miRNA | |
| MicroRNAs that showed significantly increased expression in alg-5(tm1163), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-5(tm1163)_upregulated_miRNA | |
| MicroRNAs that showed significantly decreased expression after animals were exposed to 1 mg per liter multi-walled carbon nanotubes (MWCNTs) from L1 larva to young adult. | DESeq, cut-off of 2-fold change. | WBPaper00045019:MWCNT_downregulated | |
| microRNAs that showed significantly altered expression in myrf-1(ju1121) comparing to in control animals. | DESeq2, FDR < 0.05. | WBPaper00066953:myrf-1(ju1121)_regulated_miRNA | |
| MicroRNAs that showed significantly increased expression in alg-1(gk214), comparing to in N2. | DESeq2, Fold change > 1.5. | WBPaper00051404:alg-1(gk214)_upregulated_miRNA | |
| Micro RNAs that showed significantly decreased expression in day 8 adults comparing to in day 1 adults in neuron. | Differentially expressed miRNAs were identified using DEGseq based on unique molecular identifier (UMI). A minimum UMI sum of 10 in 3 replicates was set as the threshold of expression. MiRNAs with more than five reads were defined as expressed. Differential expression of miRNAs was analysed by t-test (P value < 0.05 and fold-change > 1.5 or < 0.67) after Box-Cox transformation. MiRNA targets were identified by TargetScanWorm (Release 6.2) and Pearson Correlation Coefficient smaller than -0.2. | WBPaper00066447:Day8_vs_Day1_downregulated_neuron | |
| miRNAs that showed increased expression in 8 days post L4 adult hermaphrodite eat-2(ad1116) comparing to in N2. | A fold change >= 1.5 with a minimum read count of >= 10 were used to filter the differentially expressed miRNA. The p-value cutoff was set at p <= 0.05 based on Kals Z test statistical. | WBPaper00046156:eat-2(ad1116)_Day8_upregulated | |
| miRNAs that showed decreased expression after 100ug\/L microcystin-LR exposure. | Differentially expressed miRNA-genes were identified using the Student t-test. Changes in miRNA gene expression were considered statistically significant if the p-value was less than 0.1 and the fold-change compared to the control was at least <= 0.83 or >= 1.2. | WBPaper00045807:microcystin-LR_downregulated_miRNA | |
| miRNA that showed significantly decreased expression in stau-1(tm2266) comparing to in N2. | Differentially expressed genes were identified using edgeR package in R. | WBPaper00049286:stau-1(tm2266)_downregulated |
8 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr13546 | Few motor neurons in addition to many other muscle and hypodermal cells. | |||
| Expr8460 | Expression seen in embryos starting at the comma stage and continuing throughout adulthood. Posterior regions: intestine, ventral nerve cord, rectum, ventral muscles and tail hypodermis. Also seen in vulval muscles from L2 till adulthood. | |||
| A total of 12 independent transgenic lines were generated via bombardment and all of them showed the similar expression patterns. Picture: Fig 1, Fig S1, Fig S2. | Expr9123 | Examination of larvae and adults showed that the reporter expression remained confined to the posterior of the animal with the exception of weak expression in more anterior intestinal cells. Signal appears to increase through the L2 stage, after which it decreases with only minimal levels detectable in the tails of adults in hermaphrodites. By contrast in males the adult tail shows high levels of expression. Stably integrated lines with a 2.26 kb fragment upstream of the mir-57 mature sequence fused with a fluorescent reporter mCherry showed expression in the posterior cells of the embryo in a variety of tissues. Automated analysis of 3D time-lapse movies followed by manual editing revealed that the reporter was expressed in a bilaterally symmetric pattern in the posterior daughters of sublineages of AB and C founder cells, beginning at about the 200-cell stage. The cells from these sublineages lie in the posterior part of the embryo only and represent a wide variety of cell types, including tail seam cells, the hypodermal cells hyp10 and hyp11, the cells producing the tail spike, rectal cells, the P11/12 cells and even body wall muscle cells. Inspection of the movies beyond the comma stage also showed expression in the intestinal cells after elongation. | ||
| Expr10363 | Inferred expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/ | |||
| Expr10362 | Inferred expression. EPIC dataset. http://epic.gs.washington.edu/ Large-scale cellular resolution compendium of gene expression dynamics throughout development. This reporter was inferred to be expressing in this cell or one of its embryonic progenitor cells as described below. To generate a compact description of which cells express a particular reporter irrespective of time, the authors defined a metric "peak expression" for each of the 671 terminal ("leaf") cells born during embryogenesis. For each of these cells, the peak expression is the maximal reporter intensity observed in that cell or any of its ancestors; this has the effect of transposing earlier expression forward in time to the terminal set of cells. This metric allows straightforward comparisons of genes' cellular and lineal expression overlap, even when the expression occurs with different timing and despite differences in the precise time point that curation ended in different movies, at the cost of ignoring the temporal dynamics of expression, a topic that requires separate treatment. For simplicity, the authors use the term "expressing cells" to mean the number of leaf cells (of 671) with peak expression greater than background (2000 intensity units) and at least 10% of the maximum expression in that embryo. Quantitative expression data for all cells are located here: ftp://caltech.wormbase.org/pub/wormbase/datasets-published/murray2012/ | |||
| Picture: Fig 1C, 1D. | Expr9124 | This method lacks the cellular resolution obtained through the automated lineaging system, but staining was clearly most pronounced in the posterior of the embryo in a pattern consistent with the results of the reporter assay, while no apparent staining was observed in the mir-57 deletion strain. | ||
| Expr2487 | Intense signals were detected in embryos, larval stages (L1, L2, L3, L4), adults, and glp-4(bn2) adults. | |||
| Expr10933 |