Genomics
1 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F37B4.15.1 | F37B4.15.1 |
186
 |
V: 2892227-2892624 |
Other
1 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F37B4.15 | F37B4.15 |
186
|
V: 2892227-2892243 |
19 Allele
| Public Name |
|---|
| gk963301 |
| gk963591 |
| gk963553 |
| gk964259 |
| gk963850 |
| gk963027 |
| gk962689 |
| gk962688 |
| WBVar02124613 |
| WBVar02124042 |
| WBVar02122644 |
| WBVar02043266 |
| gk229585 |
| gk229586 |
| gk229584 |
| WBVar01738678 |
| WBVar01738677 |
| gk741713 |
| WBVar02104330 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00235329 | 2892227 | 2892624 | 1 |
1 Downstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrV_2892625..2893275 | 651 | V: 2892625-2893275 | Caenorhabditis elegans |
9 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts that showed significantly increased expression after animals were treated with 50uM Rifampicin and 250uM Allantoin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rifampicin-Allantoin_upregulated | |
| Transcripts that showed significantly increased expression after animals were treated with 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Psora-Allantoin_upregulated | |
| Transcripts that showed significantly altered expression at URX, AQR, and PQR neurons in camt-1(ok515) animals comparing to in wild type AX1888-1 strain. | RNA-seq data were mapped using PRAGUI - a Python 3-based pipeline for RNA-seq data analysis. | WBPaper00061902:camt-1(ok515)_regulated_URX-AQR-PQR | |
| 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 | |
| Acidic Environment: PH 4.33 vs. PH 6.33. | Transcripts that showed significantly increased expression after 3 hours of exposure to acidic environment (PH 4.33), comparing to control animals exposed to PH 6.33 environment. | DESeq2 (1.16.1). The Benjamini and Hochberg's approach was used to adjust the resulting P-values to control the false discovery rate. Corrected value of P < 0.05 and fold change > 2 were set as the threshold for significantly differential expression. | WBPaper00060434:pH4.33_vs_pH6.33_uprgulated |
| Transcripts that showed significantly increased expression in smn-1(ok355) heterozygots using balancer hT2 comparing to in N2. | DESeq v1.14.0, log2FC > 1, q <= 0.05. | WBPaper00056809:smn-1(ok355)_upregulated | |
| Transcripts that showed significantly increased expression after animals were treated with 100uM Rapamycin, 100uM Psora and 250uM Allantoin from day 1 to day 3 adult hermaphradite. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:Rapamycin-Psora-Allantoin_upregulated | |
| Bacteria infection: N.ferruginous | Transcripts that showed significantly altered expression in C. elegans wild isolate strain JU1400 infected by N.ferruginous microsporidia spores for 72 hours at 21C starting from L1 larva stage. | FDR < 0.01 | WBPaper00065086:JU1400_N.ferruginous_regulated |
| Transcripts that showed significantly increased expression in ikb-1(nr2027) animals at L1 larva stage, comparing to in N2 animals. | Differentially expressed genes between wild type and knockouts were explored using DESeq2 R package (v.1.20.0) considering a threshold of adjusted p value < 0.01. | WBPaper00060445:ikb-1(nr2027)_upregulated_L1 |
2 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2021648 | 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). | |||
| Expr2003433 | 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_2890030..2892226 | 2197 | V: 2890030-2892226 | Caenorhabditis elegans |
