Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:K08G2.5.1 | K08G2.5.1 |
1080
 |
V: 15856754-15858392 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:K08G2.5 | K08G2.5 |
999
|
V: 15856828-15857012 |
33 Allele
| Public Name |
|---|
| gk963271 |
| gk964458 |
| gk964459 |
| WBVar02124261 |
| otn12468 |
| WBVar00245553 |
| WBVar00245552 |
| WBVar00245551 |
| WBVar01976006 |
| WBVar01976005 |
| otn13409 |
| otn2142 |
| WBVar01591472 |
| WBVar01591473 |
| WBVar02121286 |
| WBVar00025850 |
| WBVar01777433 |
| WBVar01777434 |
| WBVar01800621 |
| otn4458 |
| WBVar01800620 |
| ttTi13723 |
| WBVar01745738 |
| gk256687 |
| gk256686 |
| gk764609 |
| gk315540 |
| gk700898 |
| gk700899 |
| gk631860 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00005364 | 15856754 | 15858392 | -1 |
3 Data Sets
| Name | URL |
|---|---|
| WormBaseAcedbConverter | |
| GO Annotation data set | |
| C. elegans genomic annotations (GFF3 Gene) |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrV_15856149..15856753 | 605 | V: 15856149-15856753 | Caenorhabditis elegans |
10 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts that showed significantly increased expression in L1 neural cells comparing to in adult neural cells. | DESeq2 (v1.18.1) fold change > 2, P-adj<0.05, using BenjaminiHochberg correction. | WBPaper00060811:L1_vs_adult_upregulated_neural | |
| 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 | |
| adult vs dauer larva | Transcripts that showed differential expression in adult vs dauer lava in N2 animals at 20C. | N.A. | WBPaper00050488:adult_vs_dauer_regulated_N2_20C |
| mRNAs that showed decreased expression in 1 cell mebryo comparing to in oocyte, according to RNAseq analysis. | Gaussian error propagation. As cutoff for the up-regulated genes authors used log2 fold change > 1 and P < 0.05 and as cutoff for the down-regulated genes authors used log2 fold change < -1 and P < 0.05. | WBPaper00045420:fertilization_downregulated_transcript | |
| Osmotic stress | Transcripts that showed significantly altered expression with 500 mM salt (NaCl) vs 100 mM salt when food was present | DESeq(version 1.10.1), FDR < 0.05. | WBPaper00050726:OsmoticStress_regulated_Food |
| Neuronally enriched transcripts according to a comparison of neuronal nuclei IP samples to total nuclei using isolation of nuclei from tagged specific cell types (INTACT) technology. | DESEQ2, fold change > 2 and FDR < 0.01. | WBPaper00062103:neuron_enriched | |
| Transcripts that showed differential expression in dauer mir-34(gk437) vs dauer mir-34(OverExpression) animals at 20C. | N.A. | WBPaper00050488:mir-34(gk437)_vs_mir-34(OverExpression)_regulated_dauer_20C | |
| Genes that showed significantly increased expression level in rsr-2(RNAi) animals comparing to in gfp(RNAi) control. | Fold change > 1.2 or < 0.8. | WBPaper00042477:rsr-2(RNAi)_upregulated_TilingArray | |
| Transcripts that showed significantly decreased expression in set-2(zr2012) 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(zr2012)_downregulated | |
| Single-cell RNA-Seq cell group 81_0 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:81_0 |
2 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1154044 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2016390 | 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). |