Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:Y41C4A.22.1 | Y41C4A.22.1 |
369
 |
III: 11695275-11696484 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:Y41C4A.22 | Y41C4A.22 |
264
|
III: 11695342-11695420 |
31 Allele
| Public Name |
|---|
| gk963887 |
| gk964363 |
| gk964364 |
| gk963799 |
| WBVar00180293 |
| WBVar00180294 |
| WBVar00180292 |
| WBVar01646695 |
| gk337638 |
| tm8951 |
| WBVar01448902 |
| gk464095 |
| gk408119 |
| WBVar01939854 |
| gk562399 |
| gk384905 |
| gk656217 |
| WBVar01270447 |
| WBVar01270446 |
| WBVar00566204 |
| WBVar02057340 |
| WBVar01852392 |
| WBVar01852391 |
| WBVar01919420 |
| WBVar01852390 |
| WBVar01507925 |
| WBVar01542354 |
| WBVar01952881 |
| gk186740 |
| WBVar01548869 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00194866 | 11695275 | 11696484 | 1 |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIII_11696485..11696572 | 88 | III: 11696485-11696572 | Caenorhabditis elegans |
14 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 | |
| Single-cell RNA-Seq cell group 71_0 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:71_0 | |
| Transcripts enriched in ASG according to single cell RNAseq. | Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. | WBPaper00061651:ASG_enriched | |
| 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 detected in body muscle nuclei according to a nuclear FACS-based strategy. | Cufflinks | WBPaper00065120:body-muscle-transcriptome | |
| Transcripts that showed significantly decreased expression in hpl-2(tm1489) comparing to in N2 animals. | DESeq2, adjusted p-value < 0.05, log2 fold change > 2 or < -2. | WBPaper00054493:hpl-2(tm1489)_downregulated | |
| Transcripts of coding genes that showed significantly increased 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_enriched_coding-RNA | |
| moderate static magnetic field | Transcripts that showed significantly decreased expression after exposure to moderate static magnetic field. | N.A. | WBPaper00064509:static-magnetic-field_downregulated |
| Transcripts that showed significantly increased expression in cco-1/cox-5B(RNAi) animals comparings to animals injected with vector control. | LimmaVoom. The genes with a BenjaminiHochbergadjusted P value < 0.05 were defined as statistically significant. Genes whose expressions were significantly upregulated with log2FC > 0.393. | WBPaper00064637:cox-5B(RNAi)_upregulated | |
| Transcripts that showed significantly increased expression in FACS sorted neuron cells (labelled by pan-neuronal GFP) from edIs6[unc-119::GFP + rol-6(su1006)]; thoc-5(wy822) comparing to in edIs6. | DESeq2, log2 fold change > 2, adjusted p-value < 0.005. | WBPaper00055103:thoc-5(wy822)_upregulated | |
| Transcripts that showed significantly decreased 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)_downregulated | |
| Top 300 transcripts enriched in ASGL, ASGR 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:ASG | |
| Transcripts enriched in PHB according to single cell RNAseq. | Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. | WBPaper00061651:PHB_enriched | |
| Transcripts that showed significantly decreased 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)_downregulated |
3 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1159848 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr2007429 | 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). | |||
| Expr2025665 | 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_chrIII_11695170..11695274 | 105 | III: 11695170-11695274 | Caenorhabditis elegans |
