Immune Signature Score

Score immune-cell signature enrichment from standardized gene expression.

Description

An immune-signature summary can average already standardized marker expression.

An immune-signature summary can average already standardized marker expression. Equal weighting makes the result dependent on the chosen genes and their upstream reference distributions.^[1]

Score immune-cell signature enrichment from standardized gene expression.

When to use Immune Signature Score

Use this tool to score immune-cell signature enrichment from standardized gene expression.

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.

How to use Immune Signature Score and understand its results

Prepare the upstream counts, expression values, sequences or record lists requested by this tool. Keep corresponding features in the same order and confirm count units, transformations and caller-selected criteria.
Enter signatureZScores, minimumMeanZ using the field table and calculation rules, then run the tool.
Read meanSignatureZ, passes. 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
signatureZScores	Signature z scores	list of number	Required
minimumMeanZ	Minimum mean z	number	Required

Enter a nonempty finite z-score list and finite minimum criterion. Compute the arithmetic mean and compare inclusively. Signed and zero scores are accepted.

meanSignatureZ=ΣsignatureZ/n; passes=(mean≥minimumMeanZ)

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

Output field	Meaning	Value type
meanSignatureZ	Mean signature z	number
passes	Passes	boolean

json

{
  "input": {
    "signatureZScores": [
      1,
      2,
      -1
    ],
    "minimumMeanZ": 0.5
  },
  "output": {
    "meanSignatureZ": 0.6666666666666666,
    "passes": true
  }
}

Limitations and assumptions

The tool does not calculate z-scores, choose markers or estimate immune-cell fractions. This is a supplied-signature mean, not a calibrated enrichment or deconvolution model.

Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. 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 Expression Zscore: Map standardized expression to a clipped diverging-color coordinate. For a complementary task, use Tumor Purity Proxy: Compute a caller-supplied marker-based tumor purity proxy, not a clinical ESTIMATE score.

References

Immune Signature Score — tool.io

Similar or alternative tools

Expression Zscore
Map standardized expression to a clipped diverging-color coordinate.
Tumor Purity Proxy
Compute a caller-supplied marker-based tumor purity proxy, not a clinical ESTIMATE score.