Analysis Tools · MVA · BUB1B · reanalysis
Rapamycin in human fibroblasts: BUB1B locus RNA signal
- Archived result
- Executed reanalysis
What it is not. 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.
Dates, kept apart
- Archived result recorded
- 2026-10-10 (snapshot mva-results-2026-10-17-immunotherapy-audit-v1, data as of 2026-10-17)
- Executions
- Execution time unknown · record packaged 2026-10-24 23:32:43 UTC · this platform
- Execution time unknown · record packaged 2026-10-24 23:32:43 UTC · this platform
- 2026-10-24 20:35:58 UTC · research repository
- 2026-10-22 18:59:19 UTC · research repository
- Repository commit
a434af9- This page rendered
- · a view date, not an execution or publication date
Values read from the files
Read from the verified outputs of execution stackfire-20261024-python312 (CPython 3.12.3, execution time unknown), whose artifacts match the archive exactly or after the documented normalisation shown in the execution record. Nothing is typed into this page.
Archived result · October 17 snapshot
Record MVA-RAP-GSE65145-001 of the frozen evidence snapshot, exactly as published on the case page. Status in the snapshot: Completed; decision: Conditional.
- Evidence class
- 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.
- 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.
- 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.
- Provenance in the snapshot
MVA_GSE65145_BUB1B_2026-10-10.zip/gse65145_bub1b_results.json· SHA-256e71199b4f23c6315f02febfd18aac8b9bcd7e7f8bb05a7a7b624ad874d54d3b6All 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.
| Row | Biological replicate 1 | Biological replicate 2 | Note |
|---|---|---|---|
| Proliferative vehicle | 6.227185 | 5.570779 | 10% FBS; DMSO vehicle. |
| Reduced serum | 1.2674783 | 0.9291951 | 0.5% FBS for five days; not matched for cell-cycle distribution. |
| Rapamycin 500 nM | 3.7114706 | 3.198672 | 500 nM for five days; 10% FBS. Mean is 0.585706 times proliferative control. |
Archive versus execution
The values the frozen snapshot shows, compared with the values read from the executed outputs. Exact where the snapshot stores the full number; otherwise within the decimal places the snapshot itself used.
| Check | Archived | Executed | Tolerance | Result |
|---|---|---|---|---|
| Rap / Pro ratio quoted in the snapshot finding (0.585706) versus the executed ratio | 0.585706 | 0.5857063642506453 | ± 5e-7 | agrees |
| Percent lower quoted in the snapshot finding (41.43%) versus the executed percent difference | -41.43 | -41.42936357493547 | ± 0.005 | agrees |
| Mean of the two rapamycin chart values versus the executed mean RPKM | 3.4550713 | 3.4550713 | ± 0.000001 | agrees |
Execution records
Each row is a run with a record. “Match” means the output bytes hash to the archived value: deterministic computation reproduced, nothing more.
| Execution / record time | What ran | Environment | Inputs | Artifacts versus archive | Record |
|---|---|---|---|---|---|
| Execution time unknownRecord packaged The original executedAt value was generated by the packaging script, not captured from the pipeline. It is preserved as recordedAt; the actual execution time is unknown.This platform | Execution on this platform (execution time unknown, CPython 3.13.17)Same fresh inputs, CPython 3.13.17 in a new virtual environment: interpreter deliberately outside the pinned version to show which artifact depends on it. | CPython 3.13.17 not the pinned interpreter pandas 2.2.3 · numpy 2.3.5 · scipy 1.17.0 · openpyxl 3.1.5 Isolated virtual environment | 14 / 14 verified by SHA-256Inputs fetched from the public URLs of input_manifest.json over the network, plus the two bundled public references; every byte count and SHA-256 compared with the manifest. |
|
Record (JSON) |
| Execution time unknownRecord packaged The original executedAt value was generated by the packaging script, not captured from the pipeline. It is preserved as recordedAt; the actual execution time is unknown.This platform | Execution on this platform (execution time unknown, CPython 3.12.3)Fresh network downloads of all 12 public inputs on 2026-10-24, each verified against input_manifest.json; system CPython 3.12.3 in a new virtual environment (the pinned 3.12.14 build was not available on this host). | CPython 3.12.3 not the pinned interpreter pandas 2.2.3 · numpy 2.3.5 · scipy 1.17.0 · openpyxl 3.1.5 Isolated virtual environment | 14 / 14 verified by SHA-256Inputs fetched from the public URLs of input_manifest.json over the network, plus the two bundled public references; every byte count and SHA-256 compared with the manifest. |
|
Record (JSON) |
| Research repository | Deterministic replay by the research repository (October 24, 2026)Run in the existing, non-isolated Python 3.12.14 environment before the sensitivity audit. | CPython 3.12.14 pandas 2.2.3 · numpy 2.3.5 · scipy 1.17.0 · openpyxl 3.1.5 Existing environment, not isolated | 14 / 14 verified by SHA-256Previously downloaded public cached bytes, each verified against the unchanged manifest; not a fresh network download. |
|
Record (JSON) At the commit |
| Research repository | Clean reproduction by the research repository (October 22, 2026)Recorded in the research repository. Successful computational reproduction under the stated input boundaries, not biological validation. | CPython 3.12.14 pandas 2.2.3 · numpy 2.3.5 · scipy 1.17.0 · openpyxl 3.1.5 Isolated virtual environment | 12 / 12 verified by SHA-256All 12 remote inputs fetched sequentially into a brand-new isolated virtual environment and verified against input_manifest.json. |
|
Record (JSON) At the commit |
Traceability
- Primary source
- Gillespie et al. — rapamycin and normal human fibroblast transcription GSE65145 processed tracks; Figures 1 and 3; Figure S2; Cell culture and RNA-seq methods · DOI 10.1080/19491034.2015.1128610 · PMID 26652669
- Dataset
- GEO GSE65145: six processed bedGraph RPKM tracks and six sample metadata files, plus the archived UCSC hg19 RefSeq annotation of chr15 (bundled input).
- Biological model
- One normal human 2DD foreskin fibroblast line; no MVA genotype, no BUBR1 protein measurement.
- Samples
- Six samples: two proliferative vehicle (10% FBS, DMSO), two reduced serum (0.5% FBS, five days), two rapamycin (500 nM, five days, 10% FBS). 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
- Script
track2/reproduction/gse65145/reanalyse_gse65145.py· SHA-256a66f9c10b93031ec620e812de59e717d35272657fdd0d56d6ea7c11230df807a· download- Command
python reanalyse_gse65145.py- Inputs
gse65145/GSE65145_RAW.tar· ftp.ncbi.nlm.nih.gov · 9.7 MB · SHA-256cb4be4c47a7926722374b3caea84c46c75b8d30161111b118f5e4bbf3791ff57gse65145/GSM1588051.soft· www.ncbi.nlm.nih.gov · 2.3 KB · SHA-256d7d47c2df0f85b1bc21a2fab8092dca004d8f9e2c353d1548f23471324357ffdgse65145/GSM1588052.soft· www.ncbi.nlm.nih.gov · 2.3 KB · SHA-256fcc03cc8656173a625d4d88ec52a053a989f8cf45a41404299b188c80f163843gse65145/GSM1588053.soft· www.ncbi.nlm.nih.gov · 2.3 KB · SHA-25658f75c0c0635eb9af3cd156768ec12be1357237673e022ac930115c779d16d4bgse65145/GSM1588054.soft· www.ncbi.nlm.nih.gov · 2.3 KB · SHA-256149482fa5b3da2bf7c83af91c42a6cc613095d958736bdfec1612825298440cegse65145/GSM1588055.soft· www.ncbi.nlm.nih.gov · 2.3 KB · SHA-2568ffb2fb9e2414d96e08892a560b6daa3f29028e03e197cc2c8f5a9630bcca74egse65145/GSM1588056.soft· www.ncbi.nlm.nih.gov · 2.3 KB · SHA-256150e67baf0258a5d5b8f5a9a26bf989d25da1d8a4bc9255620addaaf6b455cdbgse65145/hg19_chr15_refseq.json· api.genome.ucsc.edu · SHA-2561a0ccb6acb42734032645c6e13ddb79bd23d046689e7a5a3a17469a7475fff98Bundled public reference: Archived public annotation input. Live response includes changing download timestamp; preserve source bytes, not a regenerated analysis output.
Downloads
Provenance manifest (JSON)
Analysis (JSON)
The manifest lists sources, model, samples, parameters, script, commit, inputs, execution records and every file below with its SHA-256. Its generatedAt is when it was written, not an execution date.