Alternative 3prime Splice Shift

Detect alternative 3-prime acceptor site usage shifts.

Description

Alternative 3′ acceptor usage can change as a share of all supplied acceptor counts.

Alternative 3′ acceptor usage can change as a share of all supplied acceptor counts. This calculator specifically compares the first acceptor, retaining the rest only in the denominator.^[1]

Detect alternative 3-prime acceptor site usage shifts.

When to use Alternative 3prime Splice Shift

Use this tool to detect alternative 3-prime acceptor site usage shifts.

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 Alternative 3prime Splice 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 controlAcceptors, treatmentAcceptors, minimumShiftPoints using the field table and calculation rules, then run the tool.
Read firstAcceptorShiftPoints, 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
controlAcceptors	Control acceptors	list of number	Required
treatmentAcceptors	Treatment acceptors	list of number	Required
minimumShiftPoints	Minimum shift points	number	Required

Enter aligned lists with at least two nonnegative entries each and positive condition totals, plus a finite minimum shift criterion. Return signed treatment-minus-control first-acceptor percentage-point change and an inclusive absolute-change flag.

shiftPoints=100[treatment[0]/Σtreatment−control[0]/Σcontrol]

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

Output field	Meaning	Value type
firstAcceptorShiftPoints	First acceptor shift points	number
shifted	Shifted	boolean

json

{
  "input": {
    "controlAcceptors": [
      80,
      20
    ],
    "treatmentAcceptors": [
      40,
      60
    ],
    "minimumShiftPoints": 20
  },
  "output": {
    "firstAcceptorShiftPoints": -40,
    "shifted": true
  }
}

Limitations and assumptions

Site ordering must match across conditions. Shifts among later acceptors are not individually reported, and no annotations, replicates or significance tests are evaluated.

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 Polya Usage Shift: Detect proximal polyadenylation usage shifts between conditions. For a complementary task, use Mutually Exclusive Exon Switch: Identify reciprocal switching between mutually exclusive exons.

References

Alternative 3prime Splice Shift — tool.io

Similar or alternative tools

Polya Usage Shift
Detect proximal polyadenylation usage shifts between conditions.
Mutually Exclusive Exon Switch
Identify reciprocal switching between mutually exclusive exons.