Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:CC8.3.1 | CC8.3.1 |
242
 |
IV: 3641396-3642289 |
Other
30 Allele
| Public Name |
|---|
| gk963722 |
| WBVar00187650 |
| ttTi24916 |
| WBVar01515140 |
| WBVar01515141 |
| WBVar01515138 |
| WBVar01515139 |
| WBVar01922969 |
| WBVar02082328 |
| WBVar01922966 |
| WBVar01922967 |
| WBVar01922968 |
| WBVar01515136 |
| WBVar01515137 |
| WBVar01515134 |
| WBVar01515135 |
| WBVar02097928 |
| WBVar01515133 |
| WBVar01965954 |
| WBVar01965953 |
| WBVar02109055 |
| WBVar02109054 |
| WBVar01965952 |
| WBVar01838990 |
| WBVar01965951 |
| WBVar00571505 |
| WBVar02036854 |
| gk589973 |
| WBVar02003751 |
| ttTi24894 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00195049 | 3641396 | 3642289 | -1 |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIV_3640467..3641395 | 929 | IV: 3640467-3641395 | Caenorhabditis elegans |
12 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 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 | |
| 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 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 | |
| Starvation | Transcripts that showed significantly altered expression by starvation with 100 mM salt (NaCl) | DESeq(version 1.10.1), FDR < 0.05. | WBPaper00050726:starvation_regulated_LowSalt |
| Single-cell RNA-Seq cell group 25_0 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:25_0 | |
| Transcripts enriched in EVN neurons, by comparing expressin in EVN cells and in whole worm lysates. | DESeq was used. Genes overexpressed 2 - 11 fold in EVNs were considered differentially expressed. | WBPaper00049001:EVN_enriched | |
| Transcripts that showed significantly decreased 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)_downregulated_neuron | |
| Single-cell RNA-Seq cell group 25_1 expressed in neuron. | scVI 0.6.0 | WBPaper00065841:25_1 | |
| Top 300 transcripts enriched in IL2L, IL2R, IL2DL, IL2DR, IL2VL, IL2VR 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:IL2 | |
| Transcripts enriched in IL2_LR according to single cell RNAseq. | Genes that pass the Bonferroni threshold for multiple comparisons (q < 0.05) are significantly enriched. | WBPaper00061651:IL2_LR_enriched | |
| Transcripts that showed significantly decreased expression after exposed to 10ug per ml Ag nanoparticles from L1 larva to 1-day post L4 adult hermaphrodite stage. | edgeR, fold change > 2 (set by curator), FDR < 0.05. | WBPaper00059426:Ag-nanoparticles_downregulated |
3 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2020213 | 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). | |||
| Expr2001989 | 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). | |||
| Expr1147279 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 |