Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:T05A7.12.1 | T05A7.12.1 |
989
 |
II: 4662013-4663286 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:T05A7.12 | T05A7.12 |
783
|
II: 4662209-4662486 |
15 Allele
| Public Name |
|---|
| gk963801 |
| gk963053 |
| tm10138 |
| WBVar01437555 |
| WBVar01766312 |
| gk141271 |
| gk141272 |
| gk141273 |
| gk444756 |
| gk916246 |
| gk487386 |
| gk601102 |
| gk536769 |
| gk333171 |
| gk549653 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00271414 | 4662013 | 4663286 | -1 |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrII_4661379..4662012 | 634 | II: 4661379-4662012 | Caenorhabditis elegans |
12 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts of coding genes that showed significantly decreased expression in muscle. | DESeq2 (version 1.24.0). Transcripts with a false-discovery rate adjusted p-value less than 0.05 were considered significantly differentially expressed. | WBPaper00062325:muscle_depleted_coding-RNA | |
| 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 | |
| Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals. | DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2. | WBPaper00062159:hda-2(ok1479)_upregulated | |
| Transcripts that showed significantly increased expression in ilc-17.1(syb5296) comparing to in N2 animals at L4 larva stage. | DESeq2, fold change > 2, FDR < 0.05. | WBPaper00066594:ilc-17.1(syb5296)_upregulated | |
| Feeding for 4 hours after L1 arrest. | Transcripts that showed significantly decreased expression after 4 hours of feeding of starvation-induced arrested L1 N2 animals, comparing to animals continue to starve. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00067518:food_downregulated_N2 |
| Feeding for 4 hours after L1 arrest. | Transcripts that showed significantly decreased expression after 4 hours of feeding of starvation-induced arrested L1 rsks-1(ok1255) animals, comparing to animals continue to starve. | DESeq2, FDR < 0.05, fold change > 2. | WBPaper00067518:food_downregulated_rsks-1(ok1255) |
| Single-cell RNA-Seq cell group 40_0 expressed in endocrine. | scVI 0.6.0 | WBPaper00065841:40_0 | |
| Transcripts that showed significantly increased expression in spr-5(by101);met-2(n4256) L1 animals comparing to in N2 control. | DeSeq2 (v.2.11.40.2), p < 0.05. | WBPaper00060886:spr-5(by101);met-2(n4256)_upregulated | |
| Transcripts that showed significantly increased expression in spr-5(by101) L1 animals comparing to in N2 control. | DeSeq2 (v.2.11.40.2), p < 0.05. | WBPaper00060886:spr-5(by101)_upregulated | |
| Bacteria infection: Vibrio cholerae A1552, 8 hours at L4 larva stage. | Transcripts that showed significantly decreased expression in N2 animals infected by bacteria strain Vibrio cholerae A1552. | DESeq2 v1.36.0, fold change > 2, FDR < 0.05. | WBPaper00067803:V.cholerae_downregulated_N2 |
| Transcripts enriched in XXX according to single cell RNAseq. | Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. | WBPaper00061651:XXX_enriched | |
| Single-cell RNA-Seq cell group 150 expressed in: XXX. | CellRanger, DecontX, Monocle3, Louvain algorithm. | WBPaper00065623:150 |
2 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2005842 | 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). | |||
| Expr2024059 | 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_chrII_4663287..4663621 | 335 | II: 4663287-4663621 | Caenorhabditis elegans |
