Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:Y43F8B.29.1 | Y43F8B.29.1 |
219
 |
V: 19491602-19491820 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:Y43F8B.29 | Y43F8B.29 |
219
|
V: 19491602-19491820 |
29 Allele
| Public Name |
|---|
| gk963271 |
| gk962705 |
| gk963489 |
| gk963304 |
| WBVar02124642 |
| gk963809 |
| gk963637 |
| WBVar00091261 |
| WBVar02124842 |
| WBVar02121326 |
| WBVar02121908 |
| WBVar02124282 |
| WBVar02122044 |
| WBVar02122876 |
| WBVar02121484 |
| WBVar02122706 |
| WBVar02120531 |
| WBVar02123481 |
| WBVar02122402 |
| gk386241 |
| gk398046 |
| gk684627 |
| gk264773 |
| WBVar02074907 |
| WBVar01543514 |
| WBVar01543513 |
| WBVar00227069 |
| WBVar01523803 |
| WBVar01523804 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00219455 | 19491602 | 19491820 | 1 |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrV_19491821..19493884 | 2064 | V: 19491821-19493884 | Caenorhabditis elegans |
9 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at embryo stage. | DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. | WBPaper00056169:rrf-3(pk1426)_upregulated_embryo | |
| Transcripts that showed significantly decreased 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)_downregulated | |
| Transcripts that showed significantly increased expression in swsn-1(os22ts) comparing to in N2 animals at young adult worms. | DESeq2, FDR<0.05 and fold-change 2. (Threshold set by WormBase curator.) | WBPaper00060764:swsn-1(os22ts)_upregulated | |
| Transcripts that showed significantly increased expression in xpf-1(tm2842) comparing to in N2 animals. | DESeq2 1.14.1, fold change > 2, FDR < 0.01. | WBPaper00062497:xpf-1(tm2842)_upregulated | |
| Bacteria infection: Enterococcus faecalis OG1RF. 16 hours of exposure after L4 larva stage at 25C. | Transcripts that showed significantly increased expression in N2 animals fed by E. faecalis strain OG1RF for 16 hours after L4 larva stage at 25C. | DESeq2, fold change > 2. | WBPaper00061081:E.faecalis_upregulated_N2 |
| 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 | |
| Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at L2 larva stage. | DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. | WBPaper00056169:rrf-3(pk1426)_upregulated_L2 | |
| Transcripts that showed significantly decreased expression in dpl-1(n2994) comparing to in N2 animals at starved L1 larva stage. | A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated. | WBPaper00062056:dpl-1(n2994)_downregulated | |
| Transcripts that showed significantly increased expression in rrf-3(pk1426) comparing to in N2 at L1 larva stage. | DESeq2v 1.18.1, fold change > 1.5, adjusted p-value < 0.01. | WBPaper00056169:rrf-3(pk1426)_upregulated_L1 |
3 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2025747 | 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). | |||
| Expr1040541 | Tiling arrays expression graphs | |||
| Expr2007510 | 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). |