Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:Y38E10A.33.1 | Y38E10A.33.1 |
206
 |
II: 12679393-12679646 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:Y38E10A.33 | Y38E10A.33 |
129
|
II: 12679415-12679477 |
15 Allele
| Public Name |
|---|
| gk963801 |
| gk963053 |
| gk962684 |
| gk964116 |
| gk964188 |
| gk964189 |
| WBVar01605601 |
| gk423841 |
| gk735745 |
| gk157784 |
| gk157783 |
| WBVar00001548 |
| gk157785 |
| WBVar00230518 |
| WBVar00230519 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00271657 | 12679393 | 12679646 | -1 |
5 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Heat shock: 34C 30min. | Transcripts that showed significantly increased expression in L2 larva stage C. elegans animals after incubated in a 34C water bath for 30min. | DESeq2 v 1.18.1, fold change > 2, FDR < 0.01. | WBPaper00058955:heatshock_upregulated_CE |
| Transcripts that showed significantly decreased 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)_downregulated_neuron | |
| Transcripts that showed significantly altered expression in olrn-1(ums9) comparing to in N2 animals. | The Ballgown package from the Bioconductor software suite (version 3.8) was used to run a custom R script in R console(R Version 3.5) to analyze the differential gene expression, visualize the data, and perform statistical tests for differential expressionwith multiple test correction. A gene was considered to be differentially regulated if its fold change versus wild-type was greater thantwo, the adjusted p value was less than 0.05, and its RPKM was greater than one. | WBPaper00059567:olrn-1(ums9)_regulated | |
| Transcripts that showed significantly increased expression in adr-1(tm668) comparing to in N2. | DESeq2, p-value < 0.05 and a fold enrichment log2fold > 0.5. | WBPaper00055226:adr-1(tm668)_upregulated | |
| male sex-enriched | Comparisons were made between genotypes by subtracting the mean log value of one ratio from another, and the significance of the difference was evaluated using Student t-test for two populations. For the fem-3(gf) versus fem-1(lf) direct comparison, authors performed the same analysis, except they used a Students t-test for one population. Author chose a combination of a twofold difference with a t value exceeding 99% confidence (P < 0.01), because these criteria allowed the inclusion of essentially all genes that had previously been identified as germline-enriched in a wt/glp-4 hermaphrodite comparison. Additionally, requiring a twofold difference reduced false positives, as the number of genes with two-fold difference and a P<0.01 only included ~100 genes more than with P < 0.001, and almost all genes showed germline expression by in situ hybridization. | [cgc6390]:male_sex-enriched |
2 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2025539 | 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). | |||
| Expr2007306 | 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). |