Polya Usage Shift

Detect proximal polyadenylation usage shifts between conditions.

Description

Alternative polyadenylation can change the share of proximal versus distal sites.

Alternative polyadenylation can change the share of proximal versus distal sites. A percentage-point change preserves direction without confusing a change in proportion with fold change.^[1]

Detect proximal polyadenylation usage shifts between conditions.

When to use Polya Usage Shift

Use this tool to detect proximal polyadenylation usage shifts between conditions.

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 Polya Usage Shift 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 controlProximal, controlDistal, treatmentProximal, treatmentDistal, minimumUsageShiftPoints using the field table and calculation rules, then run the tool.
Read controlProximalPercent, treatmentProximalPercent, shiftPoints, shifted. 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
controlProximal	Control proximal	number	Required
controlDistal	Control distal	number	Required
treatmentProximal	Treatment proximal	number	Required
treatmentDistal	Treatment distal	number	Required
minimumUsageShiftPoints	Minimum usage shift points	number	Required

Supply nonnegative proximal/distal counts for each condition with positive condition totals and a finite minimum shift criterion. Calculate proximal percentages, signed treatment-minus-control shift and an inclusive absolute-shift flag.

shiftPoints=100[treatmentProximal/treatmentTotal−controlProximal/controlTotal]

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

Output field	Meaning	Value type
controlProximalPercent	Control proximal percent	number
treatmentProximalPercent	Treatment proximal percent	number
shiftPoints	Shift points	number
shifted	Shifted	boolean

json

{
  "input": {
    "controlProximal": 40,
    "controlDistal": 60,
    "treatmentProximal": 70,
    "treatmentDistal": 30,
    "minimumUsageShiftPoints": 20
  },
  "output": {
    "controlProximalPercent": 40,
    "treatmentProximalPercent": 70,
    "shiftPoints": 30,
    "shifted": true
  }
}

Limitations and assumptions

The tool compares supplied counts without annotation, replicate variation or significance testing. A shift criterion is a caller choice and is not separately required to be nonnegative.

Numeric inputs 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 Alternative 3prime Splice Shift: Detect alternative 3-prime acceptor site usage shifts. For a complementary task, use Utr Length Ratio: Compare 3-prime and 5-prime UTR lengths.

References

Polya Usage Shift — tool.io

Similar or alternative tools

Alternative 3prime Splice Shift
Detect alternative 3-prime acceptor site usage shifts.
Utr Length Ratio
Compare 3-prime and 5-prime UTR lengths.