Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:T05F1.15.1 | T05F1.15.1 |
219
 |
I: 9644416-9644728 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:T05F1.15 | T05F1.15 |
219
|
I: 9644416-9644535 |
10 Allele
| Public Name |
|---|
| gk962858 |
| gk962706 |
| gk963902 |
| gk963849 |
| gk964316 |
| gk536058 |
| gk119200 |
| WBVar02123967 |
| gk871798 |
| gk561029 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00194656 | 9644416 | 9644728 | -1 |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrI_9643835..9644415 | 581 | I: 9643835-9644415 | Caenorhabditis elegans |
8 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| 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 significantly increased expression in dpy-21(e428) comparing to in N2 during L3 stage. | DESeq v1.6.3. Fold change > 1.5. | WBPaper00050370:dpy-21(e428)_L3_upregulated | |
| Transcripts that showed significantly increased expression in alg-1(gk204) comparing to in N2 at 5-days post L4 adult hermaphrodites. | DESeq, fold change > 2, adjusted p-value < 0.05. | WBPaper00054758:alg-1(gk204)_upregulated | |
| Fungi infection: Fusarium oxysporum | Transcripts that showed significantly altered expression after infected by fungi Fusarium oxysporum from 0 t0 48 hours. | The Benjamini and Hochberg approach was used to adjust the resulting P-values for controlling the false-discovery rate. The transcripts having a false-discovery rate of < 0.05 were considered as differentially expressed. | WBPaper00053368:F.oxysporum_regulated |
| Transcripts that showed significantly decreased expression in ifo-1(kc2) comparing to in N2 animals. | ANOVA, p-value < 0.05. | WBPaper00056167:ifo-1(kc2)_downregulated | |
| Top 300 transcripts enriched in PLML, PLMR according to single cell RNAseq. | Top 300 enriched transcripts were determined by log2.ratio of the tpm in the cell type vs the tpm in the other cells * the log2 of the cell.type tpm. | WBPaper00061340:PLM | |
| Single-cell RNA-Seq cell group 100_0 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:100_0 | |
| Single-cell RNA-Seq cell group 107_0 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:107_0 |
3 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2005891 | 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). | |||
| Expr2024107 | 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). | |||
| Expr1156162 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 |