XCI Escapee Discordance

Flag XCI escapee candidates with expression skew but balanced methylation.

Description

Allelic expression and methylation contrasts summarize discordance between supplied measurements.

Allelic expression and methylation contrasts summarize discordance between supplied measurements.^[1]

Flag XCI escapee candidates with expression skew but balanced methylation.

When to use XCI Escapee Discordance

Use this tool to flag XCI escapee candidates with expression skew but balanced methylation.

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 XCI Escapee Discordance 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 expressionMajor, expressionMinor, methylationMajor, methylationMinor, minimumExpressionSkew, maximumMethylationSkew using the field table and calculation rules, then run the tool.
Read expressionSkew, methylationSkew, discordant. 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
expressionMajor	Expression major	number	Required
expressionMinor	Expression minor	number	Required
methylationMajor	Methylation major	number	Required
methylationMinor	Methylation minor	number	Required
minimumExpressionSkew	Minimum expression skew	number	Required
maximumMethylationSkew	Maximum methylation skew	number	Required

Enter finite expression/methylation pairs with each sum positive, plus finite minimum expression skew and maximum methylation skew. Return both normalized contrasts and their inclusive two-condition discordant flag. Thresholds and individual values may be signed.

expressionSkew=abs(expressionMajor−expressionMinor)/expressionTotal; methylationSkew likewise; discordant=expressionSkew≥minimumExpressionSkew AND methylationSkew≤maximumMethylationSkew

Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.

Output field	Meaning	Value type
expressionSkew	Expression skew	number
methylationSkew	Methylation skew	number
discordant	Discordant	boolean

json

{
  "input": {
    "expressionMajor": 80,
    "expressionMinor": 20,
    "methylationMajor": 50,
    "methylationMinor": 50,
    "minimumExpressionSkew": 0.6,
    "maximumMethylationSkew": 0.1
  },
  "output": {
    "expressionSkew": 0.6,
    "methylationSkew": 0,
    "discordant": true
  }
}

Limitations and assumptions

Individual values may be signed and contrasts can exceed one. No biological escape status is validated.

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. A successfully returned false flag is an evaluated outcome; its meaning is explained above.

Alternative or Complementary methods

Use X-Inactivation Skew: Classify X-inactivation skew from allele counts. For a complementary task, use Allele–Methylation Coupling: Detect allele-specific methylation from phased read counts.

References

XCI Escapee Discordance — tool.io

Similar or alternative tools

X-Inactivation Skew
Classify X-inactivation skew from allele counts.
Allele–Methylation Coupling
Detect allele-specific methylation from phased read counts.