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0.05887936058612938, "feature_overlap_fraction": 0.060136054421768705, "overlap_bp": 3536, "boundary_distance_bp": 111783, "qualifies_at_primary_0_99": false }, { "track_row_1based_without_header": 116270, "chrom": "chr15", "start_0based": 40510701, "end_exclusive": 40557091, "anchor_overlap_fraction": 0.04367662975605695, "feature_overlap_fraction": 0.05654235826686786, "overlap_bp": 2623, "boundary_distance_bp": 101199, "qualifies_at_primary_0_99": false } ], "genomewide_correlation": "not calculated per pre-run amendment 01; shared denominator could mislead", "replication_unit": "n=2 samples/condition, one normal cell line. Features, ratios and deletions are not additional biological replicates.", "scope": "BUB1B-spanning unstranded RNA features, not BUBR1 protein, mature isoform estimates or functional rescue", "confounding_statement": "Serum-restricted quiescence is a descriptive comparator, not a cell-cycle-matched control. No causal proliferation correction, mediator inference, p-value or CI is calculated.", "unresolved": "149122 deposited rows versus 149135 probes stated in paper; unchanged unresolved discrepancy" }, "interpretation": { "stable": [ { "claim": "PTC paired median direction across all specified row/group deletions", "status": "positive_in_all_deletions", "scope": "Finite source set, not a confidence statement or exact-variant rescue prediction" }, { "claim": "GSE BUB1B-spanning Rap/Pro signal direction across specified eligible-feature, estimator and sample diagnostics", "status": "below_one_in_all_calculated_diagnostics", "scope": "One normal cell line, n=2/condition; RNA features only" } ], "changes": [ { "claim": "PTC denominator wording", "measured_variant_rows": 12, "unique_six_base_contexts": 8, "consequence": "Replace ambiguous '12 contexts' with '12 measured variant rows spanning 8 distinct contexts'; not independent biological replicates" }, { "claim": "PTC aggregation/deletion changes magnitude, not an efficacy estimate", "consequence": "Report paired-median, group-weighted and marginal-median estimands separately" } ], "insufficient": [ { "claim": "Exact-span GSE feature estimate", "status": "insufficient_no_eligible_feature" }, { "claim": "Causal cell-cycle/proliferation adjustment", "status": "not_identifiable_from_these_data", "reason": "Quiescent serum-restricted and rapamycin samples are not cell-cycle matched; no measured cell-cycle covariate adjustment" }, { "claim": "Exact BUB1B L737*/N1002K functional rescue, BUBR1 protein and clinical efficacy", "status": "not_tested" } ], "candidate_decision": "No candidate promotion. PTC remains a low-priority experimental branch; these GSE data do not support an RNA abundance-increase rationale for sirolimus.", "interval_warning": "All reported deletion/cross-sample ranges are diagnostic ranges, not confidence intervals." } }