Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:Y7A5A.20.1 | Y7A5A.20.1 |
429
 |
X: 15828359-15829355 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:Y7A5A.20 | Y7A5A.20 |
264
|
X: 15828626-15828666 |
43 Allele
| Public Name |
|---|
| gk964260 |
| gk962707 |
| gk963810 |
| gk963581 |
| gk587782 |
| gk445579 |
| gk478765 |
| gk381371 |
| gk547858 |
| gk337377 |
| gk963633 |
| gk963982 |
| WBVar02122488 |
| WBVar02121514 |
| gk304321 |
| WBVar02120897 |
| WBVar02122290 |
| gk304319 |
| gk304320 |
| WBVar01553924 |
| otn17248 |
| otn17245 |
| otn17246 |
| WBVar01760919 |
| otn17247 |
| WBVar02083532 |
| WBVar00086933 |
| WBVar00086932 |
| WBVar01679852 |
| WBVar00086935 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00219351 | 15828359 | 15829355 | 1 |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrX_15829356..15829900 | 545 | X: 15829356-15829900 | Caenorhabditis elegans |
7 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts that showed significantly increased expression in ogt-1(ok1474) neuronal cells isolated by FACs comparing to in FACs isolated neuronal cells from wild type. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00066485:ogt-1(ok1474)_upregulated_neuron | |
| Coexpression clique No. 60, 176662_at-Y53F4B.16, on the genome-wide coexpression clique map for the nematode GPL200 platform. | All available microarray datasets for the GPL200 platform (Affymetrix C. elegans Genome Array) were obtained from the GEO repository. This included 2243 individual microarray experiments. These were normalized against each other with the software RMAexpress (Bolstad, 2014). Based on these normalized values, Pearsons correlation coefficients were obtained for each probe-probe pair of the 22,620 probes represented on this array type. The resulting list of correlation coefficients was then ranked to generate the ranked coexpression database with information on each probe represented on the GPL200 platform. | WBPaper00061527:176662_at-Y53F4B.16 | |
| Transcripts that showed significantly increased expression in set-2(tm1630) animals at embryo stage, comparing to in N2 animals. | DESeq2 (v2.1.8.3) was used to determine DE genes and to generate principal component and scatter plots. DE genes with FDR < 0.05 were analysed using g:Profiler with Bonferroni correction. | WBPaper00060014:set-2(tm1630)_upregulated | |
| Transcripts that showed significantly decreased expression in whole animal day 1 N2 adults comparing to in whole animal day 8 N2 adults. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00066978:Day1Adult_vs_Day8Adult_downregulated_neuron | |
| heat-shock hlh-1 | Genes enriched in HLH-1 heat shock dataset. | A two-class unpaired analysis was performed to identify genes that are elevated 1.7-fold or greater when compared with the reference for each dataset, at a false discovery rate of 1.8% or less for M0 and 1.2% or less for the M24 datasets. | WBPaper00031003:hlh_1_enriched |
| moderate static magnetic field | Transcripts that showed significantly decreased expression after exposure to moderate static magnetic field. | N.A. | WBPaper00064509:static-magnetic-field_downregulated |
| siRNAs that showed significantly lower expression (log2fold > 2, padj < 0.01) in hermaphrodite gonad (somatic gonad plus germine) than in male gonad (somatic gonad plus germine). | DESeq2 v1.13.8, fold change > 2, FDR < 0.01. | WBPaper00056161:male_enriched_siRNA |
2 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2026690 | 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). | |||
| Expr2008449 | 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). |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrX_15827845..15828358 | 514 | X: 15827845-15828358 | Caenorhabditis elegans |
