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Two biological samples per condition.","parameters":["Anchor: NM_001211.6 (BUB1B) span on hg19","Feature selection: at least 99% reciprocal overlap with the anchor, then minimum boundary distance","Estimator: arithmetic means of RPKM as deposited; ratios of means per condition"],"whatItIsNot":"An RNA feature in normal fibroblasts, not BUBR1 protein, not an MVA model and not a rescue. Reduced serum is not a cell-cycle-matched control; proliferation confounding is unresolved.","statuses":[{"id":"archived","label":"Archived result","description":"A value read from the frozen October 17 evidence snapshot or from a result file versioned in the research repository. Nothing was recomputed here."},{"id":"executed","label":"Executed reanalysis","description":"A real run of the original pipeline with an execution record: date, interpreter and libraries, every input verified by SHA-256, and each output compared with the archived SHA-256."}],"archived":{"snapshotId":"mva-results-2026-10-17-immunotherapy-audit-v1","dataAsOf":"2026-10-17","recordedOn":"2026-10-10","record":{"id":"MVA-RAP-GSE65145-001","title":"Rapamycin in human fibroblasts: BUB1B locus RNA signal","kind":"Reanalysis","status":"Completed","recordedOn":"2026-10-10","evidence":"Public human perturbation data; descriptive locus-level RNA reanalysis, not functional rescue.","model":"Normal 2DD fibroblasts: proliferative vehicle, 0.5% serum, or 500 nM rapamycin for five days; two biological replicates per condition.","finding":"The primary BUB1B-spanning feature has a Rap/Pro mean ratio of 0.585706 (41.43% lower); reduced-serum/Pro is 0.186191. Three nearly full-span features give the same direction. This does not support an RNA-abundance-increase rationale for sirolimus in this model.","decision":"Conditional","limitations":["Unstranded genomic-span features, not direct BUBR1 protein measurements or validated mature transcript isoform estimates.","Three overlapping features are sensitivity views of the same locus, not independent biological replicates.","Two biological replicates per condition from one normal cell line; no MVA genotype and no donor-level replication.","Serum reduction is a useful control but is not matched to rapamycin for cell-cycle distribution; no causal proliferation adjustment is claimed.","Continuous 500 nM/five-day treatment; no washout, transient exposure, aneuploidy, mitotic checkpoint or rescue endpoint.","Published normalized RPKM values are used as deposited without re-alignment, count-based differential expression, an added pseudocount, p-values or rescue probabilities.","149122 rows were observed in each deposited track; the paper states 149135 probes. The 13-row difference is not resolved here.","This does not establish that BUBR1 protein falls, rule out post-transcriptional effects, or predict clinical harm or benefit."],"next":"Keep sirolimus conditional. Proposed: compare full-length BUBR1 protein and segregation errors per completed division after transient exposure and washout at matched cell-cycle distribution. Wet-lab work is deferred.","sourceIds":["gillespie-2015"],"provenance":{"artifact":"MVA_GSE65145_BUB1B_2026-10-10.zip/gse65145_bub1b_results.json","sha256":"e71199b4f23c6315f02febfd18aac8b9bcd7e7f8bb05a7a7b624ad874d54d3b6","method":"Parse six deposited hg19 RPKM tracks; require >=99% reciprocal overlap with RefSeq NM_001211.6; select minimum boundary-distance feature and calculate ratios of arithmetic means. Check all three qualifying features.","verification":"All six coordinate arrays match; each has 149122 rows. Eighteen rows overlap the anchor and three qualify. GEO sample titles and artifact hashes verified. Complete reproducible package saved separately; no human scientific review or new biological experiment is claimed."}},"chart":{"id":"rapamycin-bub1b-locus","title":"BUB1B-spanning RNA feature in normal human fibroblasts","recordId":"MVA-RAP-GSE65145-001","unit":"RPKM as deposited; genomic-span RNA feature","note":"GSE65145; two biological replicates per condition from one normal cell line. Continuous rapamycin for five days; no washout. The selected unstranded feature spans chr15:40453238–40513321 (hg19). No protein, checkpoint-rescue or statistical-significance claim. Overlapping features are not extra replicates.","baseline":null,"series":["Biological replicate 1","Biological replicate 2"],"rows":[{"label":"Proliferative vehicle","values":[6.227185,5.570779],"note":"10% FBS; DMSO vehicle."},{"label":"Reduced serum","values":[1.2674783,0.9291951],"note":"0.5% FBS for five days; not matched for cell-cycle distribution."},{"label":"Rapamycin 500 nM","values":[3.7114706,3.198672],"note":"500 nM for five days; 10% FBS. 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