Genomics
2 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:Y73C8B.9a.1 | Y73C8B.9a.1 |
96
 |
V: 3193558-3193951 |
| Transcript:Y73C8B.9b.1 | Y73C8B.9b.1 |
45
|
V: 3193907-3193951 |
Other
2 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:Y73C8B.9a | Y73C8B.9a |
96
|
V: 3193558-3193577 |
| CDS:Y73C8B.9b | Y73C8B.9b |
45
|
V: 3193907-3193951 |
10 Allele
| Public Name |
|---|
| gk963301 |
| gk963591 |
| gk963553 |
| gk964259 |
| gk963850 |
| gk963027 |
| gk962689 |
| gk962688 |
| WBVar01614918 |
| gk323855 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00235321 | 3193558 | 3193951 | 1 |
9 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| 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 | |
| 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 | |
| Germline-enriched and sex-biased expression profile cluster C. | hierarchical clustering | [cgc6390]:Cluster_C | |
| Transcripts that showed significantly increased expression in PLM neuron cells comparing to in whole animal, according to dissected single neuron RNASeq analysis. | Fold change >= 4. | WBPaper00050344:PLM-neuron_enriched | |
| Genes that were enriched in spermatogenic fem-3(q96gf) gonads comparing to in oogenic fog-2(q71), according to RNAseq analysis. | To identify differentially expressed transcripts, authors used R/Bioconductor package DESeq. | WBPaper00045521:Spermatogenic | |
| Transcripts that interact with endogenous EGL-43-GFP at L3 larva stage according to CHIP-Seq analysis. | N.A. | WBPaper00059471:EGL-43_interacting | |
| Bacteria infection: Burkholderia pseudomallei BpR15 | Genes that showed increased expression in adult animals after 8 hour exposure to B. pseudomallei R15 vs. exposure to OP50 | After array normalization, significance analysis of microarray was performed on data from individual time points (two class unpaired response) to identify genes with small but consistent changes. A false-discovery rate (FDR) of ~1% was used as criteria to consider a gene differentially regulated.Authors chose this particular FDR because it was the lowest FDR that did not significantly reduce the number of estimated true positives. | WBPaper00044091:Bpseudomallei_induced_8h |
| Bacteria infection: Burkholderia pseudomallei BpR15 | Genes that showed increased expression in adult animals after 12 hour exposure to B. pseudomallei R15 vs. exposure to OP50 | After array normalization, significance analysis of microarray was performed on data from individual time points (two class unpaired response) to identify genes with small but consistent changes. A false-discovery rate (FDR) of ~1% was used as criteria to consider a gene differentially regulated.Authors chose this particular FDR because it was the lowest FDR that did not significantly reduce the number of estimated true positives. | WBPaper00044091:Bpseudomallei_induced_12h |
| Genome-wide analysis of developmental and sex-regulated gene expression profile. | self-organizing map | cgc4489_group_16 |
2 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2026609 | 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). | |||
| Expr2008367 | 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). |