Cell Cycle Phase

Classify a cell-cycle phase from supplied G2M and S marker scores.

Description

S and G2M marker summaries can compare evidence for two cell-cycle phases.

S and G2M marker summaries can compare evidence for two cell-cycle phases. This screen uses their relative means and can leave closely balanced profiles undetermined.^[1]

Classify a cell-cycle phase from supplied G2M and S marker scores.

When to use Cell Cycle Phase

Use this tool to classify a cell-cycle phase from supplied G2M and S marker scores.

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 Cell Cycle Phase 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 g2mMarkerScores, sPhaseMarkerScores, minimumPhaseMargin using the field table and calculation rules, then run the tool.
Read g2mMean, sMean, phase. 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
g2mMarkerScores	G 2 m marker scores	list of number	Required
sPhaseMarkerScores	S phase marker scores	list of number	Required
minimumPhaseMargin	Minimum phase margin	number	Required

Enter two nonempty finite score lists and nonnegative minimum margin; lengths may differ. Compute means and apply the stated checks in order. With margin zero and equal means, the first comparison assigns G2M.

G2M if meanG2M−meanS≥margin; else S if meanS−meanG2M≥margin; else undetermined

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

Output field	Meaning	Value type
g2mMean	G 2 m mean	number
sMean	S mean	number
phase	Phase	string; one of "G2M", "S", "undetermined"

json

{
  "input": {
    "g2mMarkerScores": [
      2,
      4
    ],
    "sPhaseMarkerScores": [
      1,
      1
    ],
    "minimumPhaseMargin": 1
  },
  "output": {
    "g2mMean": 3,
    "sMean": 1,
    "phase": "G2M"
  }
}

Limitations and assumptions

Scores, marker sets and normalization are upstream. There is no explicit G1 model or calibrated phase probability, and weak absolute scores can still meet a relative comparison.

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.

Alternative or Complementary methods

Use Immune Signature Score: Score immune-cell signature enrichment from standardized gene expression. For a complementary task, use Expression Zscore: Map standardized expression to a clipped diverging-color coordinate.

References

Cell Cycle Phase — tool.io

Similar or alternative tools

Immune Signature Score
Score immune-cell signature enrichment from standardized gene expression.
Expression Zscore
Map standardized expression to a clipped diverging-color coordinate.