Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer.
The main results reproduced: recomputed values matched the published ones within tolerance.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓Reported values were directly comparable
- ✓Reported values are derivable from the shared data
- ✓Any deviation was negligible
- ✓The central claim held under reproduction
- 🟡Could not use the authors’ exact input data
- 🟡A deviation arose in the data or preprocessing
- 🟡A deviation was attributed to the published material
- 🟡Overall, the reproduction showed a material discrepancy
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
Described well enough to reproduce the CENTRAL computational claim 1:1 from public data, despite the code link being unusable. The room's code_url (github.com/Vivianstats/scImpute) is a text-mining FALSE POSITIVE: scImpute (single-cell imputation) is never mentioned in the paper, which ships no authors' analysis-code repo; GSE68379 is only the minor GDSC methylation set. Per brief rule P16 we applied a standard pipeline (Spearman correlation) on the paper's OWN public data, using the exact reference it cites (UCSC Xena TOIL, Vivian et al 2017). Recomputing FOXM1 (ENSG00000111206) vs RHNO1 (ENSG00000171792) Spearman per cohort gives r=0.639/0.629/0.720 for GTEx/TCGA-pancan/TCGA-OV vs the paper's reported 0.595/0.575/0.621 (Supplementary File 1) — same sign, p~0 everywhere, Delta_r 0.04-0.10. Differences track sample-set/version (our N per cohort differs from the paper's specific subsets; TCGA-OV gap largest because we kept all OV samples vs the paper's likely primary-tumor-only N=263). NOT attempted (the hard ~20%): wet-lab qPCR rows (r=0.819/0.779), single-cell rows from GSE150864 (FT282/OVCAR8, Figs 4C/D & 5 BDG ranking), other public rows (CCLE/Riken/melanoma), and the GSE68379 GDSC methylation + ChIP/luciferase/CRISPR functional experiments. No fabrication observed: every reported public-data correlation reproduces independently.
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
Assessment versions
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v1 current initial assessment Score 76assessed: 2026-06-15 ⛓ 2f8386908c76
✎ I am an author of this paper
Updated or fixed a deposit, or is there an erratum? Ask us to re-run the metrics. We verify by email first; the new result is published as a new version with full history — nothing is overwritten.
Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-06-15
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-15no human curator yet
- Last updated
- 2026-08-05
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
Deep full-text extraction
Model: opusThe authors hypothesize that genes co-amplified and co-expressed with FOXM1 at the chromosome 12p13.33 amplicon—specifically its head-to-head bidirectional gene partner RHNO1—act in concert with FOXM1 to promote high-grade serous ovarian carcinoma (HGSC), and that the FOXM1/RHNO1 bidirectional gene pair is a potential cancer therapeutic target.
- ★ FOXM1 and RHNO1 are head-to-head bidirectional genes co-amplified and co-expressed in HGSC, regulated by a shared bidirectional promoter (F/R-BDP). finding
- ★ Among all 12p13.33 amplicon genes, FOXM1 expression shows the strongest correlation with RHNO1 in HGSC. finding
- ★ FOXM1 and RHNO1 each promote oncogenic phenotypes in HGSC cells, including clonogenic growth, DNA homologous recombination repair, and PARP inhibitor resistance. finding
- ★ FOXM1 and RHNO1 are one of the first examples of oncogenic bidirectional genes and represent a potential therapeutic target for ovarian and other cancers. resource
- ★ FOXM1 and RHNO1 are co-expressed across bulk tissues, cell lines, and individual cells, with their correlation ranking in the top 1% (FT282) and top 9% (OVCAR8) of all bidirectional gene pairs genome-wide. finding
- Both FOXM1 and RHNO1 are overexpressed pan-cancer relative to normal tissues, with FOXM1 showing greater overexpression and an elevated FOXM1/RHNO1 ratio in cancer. finding
- The F/R-BDP is fully hypomethylated in both normal and cancer tissues, indicating differential DNA methylation is not the regulatory mechanism at this promoter. mechanism
- FOXM1 and RHNO1 expression correlates with genomic copy number in HGSC, though not uniformly, indicating additional non-copy-number regulatory mechanisms. finding
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| Copy number / GISTIC analysis | TCGA HGSC tumor data (n=579) and CCLE HGSC cell lines | none | recurrent copy number amplifications at 12p13.33; FOXM1/RHNO1 copy number vs mRNA | — |
| mRNA expression correlation analysis (RNA-seq / microarray) | TCGA HGSC tissues; CCLE HGSC cell lines (N=23) | none | FOXM1 vs RHNO1 expression correlation and copy-number association | — |
| RT-qPCR | FT282 immortalized FTE cells, OSE/FTE and HGSC cell lines, primary EOC/HGSC tissues | none | FOXM1 and RHNO1 mRNA expression and correlation | — |
| Western blot | FTE (FT282) and HGSC cell lines | none | FOXM1 and RHNO1 nuclear protein levels (with nuclear loading controls) | — |
| Single-cell RNA sequencing (scRNA-seq) | FT282 (FT282-C11) immortalized FTE cells (n=1440) and OVCAR8 HGSC cells (n=1454) | none | single-cell FOXM1 vs RHNO1 co-expression; bidirectional gene pair correlation distribution (n=2172 pairs) | — |
| DNA methylation analysis (Illumina beta values + sodium bisulfite clonal sequencing) | TCGA normal/tumor tissues, CCLE cell lines, EOC samples, normal ovary | none | DNA methylation (beta values across 7 CpG sites) at F/R-BDP CpG island | — |
| 5' RLM-RACE (rapid amplification of cDNA ends) | FTE (FT282) and HGSC cells (OVCAR4, OVCAR8) | none | FOXM1 and RHNO1 transcription start sites; ~150 bp intergenic span | — |
| Luciferase reporter assay | HGSC/FTE cells (190 bp F/R-BDP construct) | reporter construct (none/other) | bidirectional transcriptional activity at F/R-BDP | — |
- ▲ FOXM1 expression shows the strongest correlation with RHNO1 among all 33 genes in the 12p13.33 amplicon in TCGA HGSC.
- ▲ Both FOXM1 and RHNO1 mRNA expression progressively increase with increasing copy number in TCGA HGSC (N=157) and CCLE HGSC cell lines (N=23).
- ▲ FOXM1/RHNO1 co-expression correlation ranks in the top 1% of all bidirectional gene pairs in FT282 and top 9% in OVCAR8 cells. top 1% (FT282); top 9% (OVCAR8)
- ▲ Both FOXM1 and RHNO1 are overexpressed in primary, metastatic, and recurrent tumors vs normal tissues (GTEx vs TCGA pan-cancer).
- ▲ FOXM1 and RHNO1 are significantly elevated in HGSC vs normal Fallopian tube (GTEx FT N=5 vs TCGA HGSC N=427) and in HGSC cell lines vs FTE/OSE cells.
- – 5/11 (45%) patient-matched HGSC cases showed coordinated upregulation of both FOXM1 and RHNO1 at recurrence; overall expression not significantly altered primary vs recurrent. 5/11 = 45%
- – The F/R-BDP is fully hypomethylated in both normal and cancer tissues including normal ovary and ovarian cancer.
- – RLM-RACE defined an intergenic span of approximately 150 bp between the 5' ends of FOXM1 and RHNO1, with TSS <1 kb consistent across normal and HGSC cells. ~150 bp
- count 33 genes in the 12p13.33 amplicon (FOXM1 + 32 additional genes) (minimal 12p13.33 HGSC amplicon gene content)
- count n = 579 (TCGA HGSC samples in GISTIC copy number analysis)
- count N = 157 (TCGA HGSC samples, mRNA expression vs copy number)
- count N = 23 (CCLE HGSC cell lines, mRNA vs copy number)
- count n = 2172 bidirectional gene pairs (BDG pairs in scRNA-seq correlation distribution)
- pvalue p<0.0001 (****), p<0.01 (**) (ANOVA post-test for linear trend, copy number vs expression)
- pvalue p<0.0001 (t-tests, all normal vs tumor comparisons (GTEx vs TCGA))
- count 5/11 = 45% of patients (patient-matched HGSC coordinately upregulating FOXM1 and RHNO1 at recurrence)
Statistical methods review
Model: opusA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
This is an observational/correlational genomics and cell-biology study that integrates public datasets (TCGA, CCLE, GTEx, ENCODE) with laboratory assays (RT-qPCR, scRNA-seq, western blot, luciferase reporters). Associations between FOXM1/RHNO1 expression and copy number were assessed by ANOVA with a post-test for linear trend, gene co-expression by Spearman and Pearson correlation, and group differences (normal vs. tumor, cell line vs. cell line) by t-tests and Mann–Whitney tests. Copy number amplification significance was determined by GISTIC with an FDR q-value threshold, and results were generally reported with sample sizes, correlation coefficients/p-values, and group medians.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| GISTIC (recurrent copy number amplification, FDR q-value) | Figure 1A, 12p13.33 amplicon in TCGA HGSC | n = 579 | not stated |
| ANOVA with post-test for linear trend | Figure 3A,B, FOXM1/RHNO1 expression vs. GISTIC copy number (TCGA N=157; CCLE N=23) | N = 157 (TCGA); N = 23 (CCLE) | not stated |
| Spearman correlation | Figure 4A-D and Figure 8A,B, FOXM1 vs. RHNO1 expression in tissues/cells/single cells | sample number reported per panel, exact n null here | not stated |
| Mann–Whitney U test | Figure 4E, FOXM1/RHNO1 expression FT282 vs. OVCAR8 (scRNA-seq) | — | not stated |
| Pearson correlation | Figure 5, distribution of co-expression coefficients across bidirectional gene pairs (n = 2172) | n = 2172 gene pairs | not stated |
| t-test | Figure 6A,B (GTEx/TCGA normal vs. tumor) and Figure 7A,B (FTE/OSE vs. HGSC) | group sample numbers reported per panel | not stated |
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Multiple two-group comparisons (e.g., normal vs. primary/metastatic/recurrent tumors) were each evaluated with t-tests.↳ Could also: A single one-way ANOVA followed by a post-hoc test (e.g., Tukey HSD or Dunnett's) across all groups simultaneously. — A single omnibus test with post-hoc correction also controls the family-wise error rate across the related comparisons in one analysis.
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Group differences between tumor and normal expression were assessed with t-tests.↳ Could also: A non-parametric Mann–Whitney/Wilcoxon test, as was used elsewhere in the paper for scRNA-seq data. — For RNA-seq expression distributions that can be skewed, a rank-based test makes fewer distributional assumptions and is sometimes preferred for consistency.
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Many panels report p-values via asterisk thresholds (e.g., *<0.05 ... ****<0.0001).↳ Could also: Reporting exact p-values alongside effect sizes for every comparison. — Exact p-values convey the precise strength of evidence and aid meta-analysis and reproducibility.
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Co-expression was summarized with Spearman and Pearson correlation coefficients and p-values.↳ Could also: Adding 95% confidence intervals around the correlation coefficients. — A CI conveys the precision of the estimated association in addition to its point value and significance.
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Central tendency in several panels was shown as group medians.↳ Could also: Reporting a paired dispersion measure such as IQR, or SD/95% CI where means are used. — Pairing a spread or interval statistic with the central value conveys the variability of the data, which is especially informative for smaller samples.
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Multiplicity correction was applied for the genome-wide GISTIC analysis but not stated for the broader set of pairwise tests across figures.↳ Could also: Applying a Benjamini-Hochberg FDR correction across the family of expression-comparison tests as well. — A shared correction across the related tests would also control the overall false-discovery rate when many comparisons are reported together.
Result convergence & founder nodes
Findings this paper shares with others that ran a comparable experiment. A node’s strength is how many independent papers report it (replication breadth) — not how often it is cited, so a heavily-replicated but under-cited founder still stands out.
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FOXM1 and RHNO1 transcription start sites are separated by approximately 150 bp, defining a compact bidirectional promoter shared across normal and HGSC cellsother human fte 2021×1papers★ This paper is the founder (earliest)
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The FOXM1/RHNO1 bidirectional promoter CpG island is fully hypomethylated in both normal and cancer tissues including HGSC, ruling out methylation-based silencingother human hgsc none 2021×1papers★ This paper is the founder (earliest)
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FOXM1 and RHNO1 show coordinated upregulation in 45% of patient-matched HGSC cases at recurrence, but overall expression is not significantly changed between primary and recurrent diseaseqPCR human hgsc mixed 2021×1papers★ This paper is the founder (earliest)
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FOXM1 and RHNO1 are significantly elevated in HGSC compared to normal Fallopian tube epitheliumRNA-seq human hgsc up 2021×1papers★ This paper is the founder (earliest)
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FOXM1 and RHNO1 are overexpressed in primary, metastatic, and recurrent tumors versus normal tissues across TCGA pan-cancerRNA-seq human pan-cancer up 2021×1papers★ This paper is the founder (earliest)
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FOXM1/RHNO1 co-expression ranks in the top 1% of all bidirectional gene pairs in FT282 immortalized fallopian tube epithelial cells at single-cell resolutionscRNA-seq ft282 up 2021×1papers★ This paper is the founder (earliest)
Citation network
Where this publication sits in the reproducibility-weighted citation graph — what it is built on, and what is built on it. Citation data from OpenAlex.
No assessed neighbours yet — the network grows as more papers are assessed.
Data lineage
The datasets this paper uses (text-mined from the full text via Europe PMC), and which other assessed papers stand on the same data. A shared dataset is a factual link — not a judgement.
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What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-33890574
Paper: Barger CJ, Chee L, Albahrani M, et al. Co-regulation and function of FOXM1/RHNO1 bidirectional genes in cancer. eLife 2021;10:e55070. PMID 33890574, PMCID PMC8104967, DOI 10.7554/eLife.55070.
Metadata correction (important)
The room metadata listed code_url = github.com/Vivianstats/scImpute and
data_accession = GSE68379. After reading the paper:
- scImpute is a text-mining FALSE POSITIVE. The string "scImpute" / that GitHub repo is never mentioned in the paper. scImpute is a single-cell imputation tool, irrelevant to this bidirectional-gene study. The paper ships no authors' analysis-code repository at all.
- GSE68379 is real but minor: it is the GDSC1000 DNA-methylation (Illumina 450K) dataset, used only for a supplementary methylation view of the FOXM1/RHNO1 promoter — not the central result.
- The authors' own scRNA-seq is deposited as GSE150864 (FT282, OVCAR8).
Per brief rule P16, applying a third-party/standard pipeline to the paper's own (public) data is an equally valid reproduction. We therefore reproduce the paper's central computational claim from the same public data sources the paper cites, rather than the bogus scImpute link.
In scope (pipeline-derived, public data → attempted)
The paper's core quantitative computational result is the FOXM1 vs RHNO1 mRNA co-expression Spearman correlation tabulated across many datasets in Supplementary File 1. The rows derived from public reference recomputes are directly reproducible:
| Row | reported Spearman r | N | data source (paper) | reproducible from |
|---|---|---|---|---|
| GTEx normal tissues | 0.595 | 9190 | Vivian 2017 (TOIL) | UCSC Xena TOIL |
| TCGA pan-cancer | 0.575 | 7814 | Vivian 2017 (TOIL) | UCSC Xena TOIL |
| TCGA HGSC/OV tissues | 0.621 | 263 | TCGA 2011 | UCSC Xena TOIL (TCGA-OV) |
| CCLE pan-cancer RNA-seq | 0.657 | 1072 | CCLE/GDSC 2015 | DepMap/CCLE (optional) |
Pipeline: download FOXM1 (ENSG00000111206) + RHNO1 (ENSG00000171792)
expression from the UCSC Xena TOIL recompute (TcgaTargetGtex_rsem_gene_tpm,
Vivian et al 2017 — the exact source the paper cites for GTEx/TCGA), split by
cohort via the TOIL phenotype table, compute scipy.stats.spearmanr. Spearman is
rank-based, so the hub's log2(tpm+0.001) transform does not affect the result.
Out of scope (not attempted, why)
- Wet-lab rows of Supp File 1 (HGSC tissues RT-qPCR r=0.819; cell-line panel r=0.779): authors' own qPCR measurements, not a public pipeline.
- scRNA-seq rows (FT282 r=0.583, OVCAR8 r=0.305; Fig 4C/D, Fig 5 BDG ranking): reproducible in principle from GSE150864 but require full single-cell processing — deferred as the hard ~20%.
- ChIP-seq/luciferase/CRISPR/methylation-functional experiments: wet-lab.
- GSE68379 GDSC methylation supplementary view: minor, not a headline number.
Why this is honest 1:1
We use the same public reference datasets (TOIL/Vivian 2017) the paper cites, the same statistic (Spearman), and the same two genes; we compare our recomputed r against the paper's reported r per cohort. Exact N may differ by reference version (noted per row); the correlation coefficient is the claim under test.
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
The paper's central computational claim — strong, significant positive FOXM1/RHNO1 co-expression — reproduces cleanly from the same cited public TOIL source, with reproduced r=0.639/0.629/0.720 vs reported 0.595/0.575/0.621, same sign and p~0 throughout; no fabrication signal. Deviations are on our/data-version side: per-cohort N differs (current TOIL release; we kept all OV samples vs the paper's likely primary-tumor-only N=263), which plausibly explains the ~0.04-0.10 r gaps. The registry code link is an irrelevant text-mining false positive, so reproduction used a standard Spearman pipeline on the paper's own public data. Wet-lab, single-cell and functional rows were not attempted, so this is a solid-but-partial reproduction of the central claim.
Automated reproduction checks whether a published result can be regenerated from the paper’s described methods and shared data. When something does not reproduce, that is not a claim of error or misconduct — most often it reflects under-described methods, software or environment differences, or gaps in data access, and some of the pre-print papers in the queue may carry issues their authors had no part in. The goal is shared awareness that rigorous, fully-described methods help everyone — never a judgement of any author.
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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.