{
  "comparison_id": "oncoref.native-gene-tpm-normal-reference.2026-11-09.1",
  "unit": "TPM",
  "purpose": "Source-native gene-abundance screening; not calibrated cross-study differential expression",
  "compatibility_basis": [
    "Linear transcript-per-million gene abundance; reject microarray proxies, CP10K, CPM proxies, nTPM, pTPM and gene-feature-count TPM",
    "Current exact locus mapping; ambiguous duplicate vectors quarantined; protein-identical loci summed only in the same sample/context with all members measured",
    "Pinned tumor matrices and per-sample quality selection from the existing source-scale registry",
    "Complete 36-context combined nonreproductive normal anatomy panel, plus observed native-TPM normal immune and brain measurements"
  ],
  "expression_bounds": {
    "target_maximum": "max(tumor, adult reproductive, developmental) >= 1 and above every measured nonreproductive normal and Disposable value on the comparison scale.",
    "disposable_cap_tpm": 32.0,
    "disposable_cap_ntpm": 32.0,
    "cap_scope": "Each source scale separately; a screening convention, not a tolerance.",
    "failure": "Other:Expression"
  },
  "disposable_ntpm_tissues": [
    "appendix",
    "gallbladder",
    "tonsil"
  ],
  "normal_statistic": "Maximum supported context statistic: tissue/subregion means, GTEx v11 donor medians, and supported immune summaries including DICE third-highest TPM",
  "batch_corrected": false,
  "limitations": [
    "Quantifier, library preparation and study effects are retained; the fold rule is a screening convention",
    "A maximum of tissue summaries is not a maximum over every healthy donor",
    "Other assay scales continue to enforce the existing shared normal screen independently"
  ],
  "participant_identity": "Shared sample_identities API joins curated case/donor mappings and documented TCGA, TARGET, MMRF and Treehouse identifiers. Every sample retains identity status, basis and references. Unresolved or conflicting identities support only the single-sample route.",
  "participant_identity_policy": "oncoref.patient-identity.2026-11-10.1",
  "normal_sources": [
    {
      "source": "rna_tissue_hpa",
      "version": "v23",
      "url": "https://v23.proteinatlas.org/download/rna_tissue_hpa.tsv.zip",
      "path": "tmp/target-rebuild-inputs/rna_tissue_hpa.tsv.zip",
      "sha256": "47f325ce9281ba94c64d8d0ba0c27bc3f2f6ed668fa8c8f1a9a10671e690025c",
      "bytes": 6661353
    },
    {
      "source": "rna_tissue_gtex",
      "version": "v23",
      "url": "https://v23.proteinatlas.org/download/rna_tissue_gtex.tsv.zip",
      "path": "tmp/target-rebuild-inputs/rna_tissue_gtex.tsv.zip",
      "sha256": "820cc275a8f3f4d162a2e0b87ed75f9a0e176538fa336320ea3179f9e459d881",
      "bytes": 5960172
    },
    {
      "source": "rna_brain_gtex",
      "version": "v23",
      "url": "https://v23.proteinatlas.org/download/rna_brain_gtex.tsv.zip",
      "path": "tmp/target-rebuild-inputs/rna_brain_gtex.tsv.zip",
      "sha256": "4bcaf4dc8446116f6426a9e447a22b90acc6e05872c758b366e662c0a6c56592",
      "bytes": 1633631
    }
  ],
  "method_references": [
    "https://v23.proteinatlas.org/about/assays%2Bannotation",
    "https://pmc.ncbi.nlm.nih.gov/articles/PMC5903355/"
  ],
  "required_contexts": [
    "adipose tissue",
    "adrenal gland",
    "amygdala",
    "basal ganglia",
    "bone marrow",
    "cerebellum",
    "cerebral cortex",
    "choroid plexus",
    "colon",
    "duodenum",
    "esophagus",
    "heart muscle",
    "hippocampal formation",
    "hypothalamus",
    "kidney",
    "liver",
    "lung",
    "lymph node",
    "midbrain",
    "pancreas",
    "parathyroid gland",
    "pituitary gland",
    "rectum",
    "retina",
    "salivary gland",
    "skeletal muscle",
    "skin",
    "small intestine",
    "smooth muscle",
    "spinal cord",
    "spleen",
    "stomach",
    "thymus",
    "thyroid gland",
    "tongue",
    "urinary bladder"
  ],
  "tumor_matrix_cache_sha256": "a2fbcab7e2395f4ab4ab99fc057ee18b043e0999d52d297bd0d92ed00218d9ab"
}