Genomics
2 Transcripts
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| Transcript:F22B3.5a.1 | F22B3.5a.1 |
899
 |
IV: 11415598-11416824 |
| Transcript:F22B3.5b.1 | F22B3.5b.1 |
606
|
IV: 11415632-11416561 |
Other
2 CDSs
| WormMine ID | Sequence Name | Length (nt) | Chromosome Location |
|---|---|---|---|
| CDS:F22B3.5a | F22B3.5a |
636
|
IV: 11415598-11415695 |
| CDS:F22B3.5b | F22B3.5b |
606
|
IV: 11415632-11415695 |
23 Allele
| Public Name |
|---|
| gk964278 |
| gk964078 |
| gk964500 |
| gk962765 |
| gk963703 |
| gk963917 |
| WBVar02121216 |
| tm10585 |
| WBVar02124419 |
| WBVar02124420 |
| otn18203 |
| WBVar02076833 |
| WBVar01454236 |
| gk888237 |
| gk761176 |
| gk212657 |
| gk794169 |
| gk625326 |
| gk516376 |
| gk212655 |
| WBVar00192039 |
| gk713302 |
| gk212656 |
1 Chromosome Location
|
Feature . Primary Identifier |
Start | End | Strand |
|---|---|---|---|
| WBGene00009036 | 11415598 | 11416824 | -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_chrIV_11415021..11415597 | 577 | IV: 11415021-11415597 | Caenorhabditis elegans |
11 Expression Clusters
| Regulated By Treatment | Description | Algorithm | Primary Identifier |
|---|---|---|---|
| Transcripts that showed significantly increased expression in csr-1a(tor159) comparing to in N2 at 25C. | DESeq2, fold change > 2, p-value < 0.05. | WBPaper00061753:csr-1(tor159)_upregulated_25C | |
| Transcripts that showed significantly decreased expression in eat-2(ad1116) comparing to in N2 at 3-days post L4 adult hermaphrodite animals. | DESeq2(v1.14.1), fold change > 2, p-value < 0.05 | WBPaper00055354:eat-2(ad1116)_downregulated | |
| Up-regulated genes (fold change > 1.5) in two CoQ-deficient clk-1 mutant strains (e2519, qm30) compared to wild types N2. | Fold-changes of intensities were calculated from the arithmetic mean of gene expression values between experimental and corresponding control group. Fold change >= 1.5 was used as cut-off. | WBPaper00045774:clk-1_upregulated | |
| Significantly downregulated genes from cyc-1(RNAi) microarrays using SAM algorithm with an FDR < 0.1 from adult-only chips. | SAM algorithm with an FDR < 0.1. | WBPaper00033065:cyc-1(RNAi)_downregulated | |
| Transcripts that showed significantly increased expression in mrps-5(RNAi) comparing to in control animals. | Fold change > 4, p-value < 0.01 | WBPaper00056330:mrps-5(RNAi)_upregulated | |
| Fungi infection: Fusarium oxysporum | Transcripts that showed significantly altered expression after infected by fungi Fusarium oxysporum from 0 t0 48 hours. | The Benjamini and Hochberg approach was used to adjust the resulting P-values for controlling the false-discovery rate. The transcripts having a false-discovery rate of < 0.05 were considered as differentially expressed. | WBPaper00053368:F.oxysporum_regulated |
| Transcripts that showed significantly decreased expression in daf-2(e1370) comparing to in N2. | Student's t-test, fold change > 2, p-value < 0.05. | WBPaper00055386:daf-2(e1370)_downregulated | |
| Transcripts that showed significantly increased expression in cco-1/cox-5B(RNAi) animals comparings to animals injected with vector control. | LimmaVoom. The genes with a BenjaminiHochbergadjusted P value < 0.05 were defined as statistically significant. Genes whose expressions were significantly upregulated with log2FC > 0.393. | WBPaper00064637:cox-5B(RNAi)_upregulated | |
| Transcripts significantly enriched in AVK neurons comparing to all cell types at L1 larva stage. | edgeR, FDR < 0.001, fold change > 2. | WBPaper00055565:AVK_enriched | |
| Transcripts that showed significantly increased expression in atfs-1(et18) comparing to in N2 animals at L4 larva stage. | edgeR, fold change > 2, FDR < 0.05 | WBPaper00060909:atfs-1(et18)_upregulated | |
| Transcripts that showed more than 4 fold of expression in CB4856 comparing to in N2 animals. | DESeq2, fold change > 4. | WBPaper00053909:N2_vs_CB4856_downregulated |
4 Expression Patterns
| Remark | Reporter Gene | Primary Identifier | Pattern | Subcellular Localization |
|---|---|---|---|---|
| Expr2021065 | 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). | |||
| Expr1014360 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/levin2012 | |||
| Expr2002847 | 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). | |||
| Expr1149202 | Developmental gene expression time-course. Raw data can be downloaded from ftp://caltech.wormbase.org/pub/wormbase/datasets-published/hashimshony2015 |
1 Upstream Intergenic Region
| WormBase ID | Name | Sequence Name | Length (nt) | Chromosome Location | Organism |
|---|---|---|---|---|---|
| intergenic_region_chrIV_11416825..11417580 | 756 | IV: 11416825-11417580 | Caenorhabditis elegans |
