TET Cascade Stage
Map a cytosine modification to its TET cascade stage.
Description
DNA demethylation involves TET oxidation of 5mC and subsequent restoration of C through repair pathways.
DNA demethylation involves TET oxidation of 5mC and subsequent restoration of C through repair pathways.1
Map a cytosine modification to its TET cascade stage.
When to use TET Cascade Stage
Use this tool to map a cytosine modification to its TET cascade stage.
Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
How to use TET Cascade Stage and understand its results
- Prepare the already measured signals, counts, coordinates, fitted coefficients or sequence strings requested. Keep assay definitions, units, aligned lists and caller-selected thresholds consistent.
- Enter modification using the field table and calculation rules, then run the tool.
- Read cascadeIndex, nextStage. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| modification | Cytosine modification | string; one of "5mC", "5hmC", "5fC", "5caC", "C" | Required |
Select an exact stage enum. Return its zero-based index and next stored stage, with no next step at the terminal stage.
stages=[5mC,5hmC,5fC,5caC,C] Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| cascadeIndex | Cascade index | integer; minimum: 0; maximum: 4 |
| nextStage | Next stage | string |
{
"input": {
"modification": "5hmC"
},
"output": {
"cascadeIndex": 1,
"nextStage": "5fC"
}
}Limitations and assumptions
The return to C is not another TET oxidation reaction. No reaction kinetics or biological state is measured.
Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Extremely large text inputs are rejected. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use Hydroxymethylation Subtraction: Subtract oxBS from BS methylation to estimate 5hmC. For a complementary task, use Passive Demethylation: Model passive methylation dilution across divisions.
References
-
TET Cascade Stage — tool.io
Similar or alternative tools
- Hydroxymethylation Subtraction
Subtract oxBS from BS methylation to estimate 5hmC.
- Passive Demethylation
Model passive methylation dilution across divisions.