Passive Demethylation
Model passive methylation dilution across divisions.
Description
Passive-demethylation retention can be summarized across divisions using an assumed retained fraction.
Passive-demethylation retention can be summarized across divisions using an assumed retained fraction.1
Model passive methylation dilution across divisions.
When to use Passive Demethylation
Use this tool to model passive methylation dilution across divisions.
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 Passive Demethylation 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 initialMethylationPercent, cellDivisions, maintenanceFidelityPercent using the field table and calculation rules, then run the tool.
- Read retainedMethylationPercent, lostMethylationPoints. 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 |
|---|---|---|---|
| initialMethylationPercent | Initial methylation | number; minimum: 0; maximum: 100 | Required |
| cellDivisions | Cell divisions | integer; minimum: 0 | Required |
| maintenanceFidelityPercent | Maintenance fidelity | number; minimum: 0; maximum: 100 | Required |
Enter percentages 0–100 and nonnegative integer divisions; return remaining percentage and lost percentage points. Zero divisions retain the initial value.
remaining%=initial%×(fidelity%/100)^divisions Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| retainedMethylationPercent | Retained methylation | number; minimum: 0; maximum: 100 |
| lostMethylationPoints | Lost methylation | number; minimum: 0 |
{
"input": {
"initialMethylationPercent": 80,
"cellDivisions": 2,
"maintenanceFidelityPercent": 50
},
"output": {
"retainedMethylationPercent": 20,
"lostMethylationPoints": 60
}
}Limitations and assumptions
No strand-specific replication, selection or enzyme kinetics is modeled.
Numeric inputs, where present, must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors.
Alternative or Complementary methods
Use TET Cascade Stage: Map a cytosine modification to its TET cascade stage. For a complementary task, use Epimutation Rate: Estimate epimutation rate per site and generation.
References
-
Passive Demethylation — tool.io
Similar or alternative tools
- TET Cascade Stage
Map a cytosine modification to its TET cascade stage.
- Epimutation Rate
Estimate epimutation rate per site and generation.