Isoform TPM Share

Normalize isoform TPMs to within-gene usage percentages.

Description

Within-gene isoform shares renormalize supplied TPM values to a gene total.

Within-gene isoform shares renormalize supplied TPM values to a gene total. Those percentages use a smaller denominator than library-wide TPM.^[1]

Normalize isoform TPMs to within-gene usage percentages.

When to use Isoform TPM Share

Use this tool to normalize isoform TPMs to within-gene usage percentages.

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 Isoform TPM Share 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 isoformIds, isoformTpms using the field table and calculation rules, then run the tool.
Read isoformSharesPercent, geneTpm. 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
isoformIds	Isoform ids	list of string	Required
isoformTpms	Isoform tpms	list of number	Required

Enter aligned nonempty isoform IDs and nonnegative TPM values with a positive sum. Return shares in input order and summed gene TPM. Zero-valued isoforms have zero share; repeated IDs are not merged.

geneTPM=ΣisoformTPM; isoformShare%=100 isoformTPM/geneTPM

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

Output field	Meaning	Value type
isoformSharesPercent	Isoform shares percent	list of number
geneTpm	Gene tpm	number

json

{
  "input": {
    "isoformIds": [
      "x",
      "y"
    ],
    "isoformTpms": [
      20,
      80
    ]
  },
  "output": {
    "isoformSharesPercent": [
      20,
      80
    ],
    "geneTpm": 100
  }
}

Limitations and assumptions

The tool assumes all entries belong to the intended gene and set. It does not estimate isoform abundance, recover omitted isoforms or assess changes across conditions.

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 Transcripts Per Million: Normalize transcript length-adjusted abundances to one million TPM. For a complementary task, use Polya Usage Shift: Detect proximal polyadenylation usage shifts between conditions.

References

Isoform TPM Share — tool.io

Similar or alternative tools

Transcripts Per Million
Normalize transcript length-adjusted abundances to one million TPM.
Polya Usage Shift
Detect proximal polyadenylation usage shifts between conditions.