Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:B0244.16.1 | B0244.16.1 |
1083
 |
III: 5740966-5742822 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:B0244.16 | B0244.16 |
1083
|
III: 5740966-5741067 |
28 Allele
| Public Name |
|---|
| gk964518 |
| gk175315 |
| gk964338 |
| gk964339 |
| WBVar01263865 |
| tm10042 |
| WBVar01330430 |
| ttTi12265 |
| WBVar01445891 |
| gk498095 |
| WBVar00061587 |
| WBVar00061592 |
| WBVar00061597 |
| gk914637 |
| gk636182 |
| gk378032 |
| WBVar00061602 |
| gk656711 |
| gk524640 |
| gk688072 |
| gk854845 |
| gk770231 |
| gk667650 |
| gk477945 |
| WBVar01644809 |
| WBVar01644810 |
| WBVar01644811 |
| WBVar01396838 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00271577 | 5740966 | 5742822 | 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_chrIII_5742823..5743383 | 561 | III: 5742823-5743383 | Caenorhabditis elegans |
8 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 | |
| Bacteria: E.faecalis strain OG1RF | Transcripts that showed significantly increased expression after infection by E. faecalis OG1RF. | Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05. | WBPaper00059754:E.faecalis_OG1RF_upregulated |
| Transcripts that showed significantly increased expression in pri-1(RNAi) animals comparing to in N2 animals fed with empty vector. | Differential expression analysis was performed quasi-likelihood F-test with the generalized linear model (GLM) approach in edgeR ver 3.32.1. FDR < 0.05, fold change > 2. | WBPaper00066418:pri-1(RNAi)_upregulated | |
| Transcripts that showed significantly increased expression in hda-2(ok1479) comparing to in N2 animals. | DESeq2 (version 1.28.1), FDR < 0.01, fold change > 2. | WBPaper00062159:hda-2(ok1479)_upregulated | |
| Bacteria: P.aeruginosa strain PA14 | Transcripts that showed significantly increased expression after infection by P. aeruginosa PA14. | Ballgown was used to calculate differential expression of genes using FPKM data and to generate tables with fold change and P values. Genes were shortlisted with a cutoff of 2-fold change and P values of less than 0.05. | WBPaper00059754:P.aeruginosa_PA14_upregulated |
| Transcripts that showed signicantly increased expression in unc-25(e156) comparing to in N2 animals. | DESeq R package (1.18.0), fold change > 2, FDR < 0.05. | WBPaper00065734:unc-25(e156)_upregulated | |
| Top 300 transcripts enriched in B cell, F cell, K cell, K' cell, U cell, Y cell 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:B_F_K_Kp_U_Y | |
| Top 300 transcripts enriched in AMshL, AMshR 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:AMsh |
2 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2018301 | 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). | |||
| Expr2000084 | 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). |
5 GO Annotation
| Annotation Extension | Qualifier |
|---|---|
| involved_in | |
| located_in | |
| enables | |
| involved_in | |
| located_in |
