Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:M03F8.7.1 | M03F8.7.1 |
877
 |
V: 5936939-5939188 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:M03F8.7 | M03F8.7 |
720
|
V: 5937096-5937187 |
37 Allele
| Public Name |
|---|
| gk963301 |
| gk963591 |
| gk963553 |
| gk963042 |
| gk963041 |
| gk964259 |
| gk964351 |
| gk963850 |
| WBVar01862456 |
| WBVar01862458 |
| WBVar01862457 |
| WBVar00209951 |
| WBVar00209950 |
| gk902212 |
| gk800838 |
| gk935184 |
| gk478103 |
| gk693827 |
| gk394439 |
| gk582579 |
| gk506140 |
| gk518334 |
| gk847931 |
| gk333369 |
| gk506141 |
| gk936843 |
| gk889809 |
| gk710622 |
| gk808235 |
| gk714339 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00189957 | 5936939 | 5939188 | 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_5939189..5940021 | 833 | V: 5939189-5940021 | Caenorhabditis elegans |
5 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| 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 | |
| Transcripts that showed significantly increased 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)_upregulated_neuron | |
| Transcipts that showed significantly increased expression in old (days 24, 14, and 9 of adulthood) octr-1(ok371) comparing to in N2 at 25C. | DESeq2 v1.31.16, fold change > 2, FDR < 0.05 | WBPaper00068082:octr-1(ok371)_upregulated_old_25C | |
| Genes enriched in AMsh glia. | Two different statistical methods were used for differential gene expression analysis, DESeq and voom. For DEseq analysis, DESeq2 was applied to normalize count matrix and to perform differential gene expression on the counts using negative binomial distribution; for voom analysis, edgeR was applied to normalize count matrix, and voom was applied for gene differentiation analysis. Significant genes from both analyses were combined. To identify transcripts enriched in AMsh glia compared to other cells (control AMsh versus control non-AMsh), authors used a fold change of 3.5 and an adjusted p value threshold of <0.05. | WBPaper00049489:AMsh-glia_enriched | |
| Transcripts that showed significantly increased expression in mes-4(bn73) comparing to in control animals in early germ cells (EGCs) at L1 larva stage. | DESeq2(v1.32.0), FDR < 0.05. | WBPaper00064315:mes-4(bn73)_upregulated_EGCs |
3 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr1154580 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 | |||
| Expr1026943 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2005186 | 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_chrV_5936792..5936938 | 147 | V: 5936792-5936938 | Caenorhabditis elegans |
