Interaction of alphaPIX (ARHGEF6) with beta-parvin (PARVB) suggests an involvement of alphaPIX in integrin-mediated signaling.
Part of the results reproduced; minor but material deviations remained.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓No authors-side cause for any deviation
- ✓Any deviation was negligible
- 🔴Could not use the authors’ exact input data
- 🔴Reported values were only indirectly comparable
- 🟡A deviation arose in the data or preprocessing
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡The central claim did not (fully) hold under reproduction
- 🟡Overall, the reproduction showed a material discrepancy
▸Reproduction agent’s raw note
DROP (non_pipeline). PMID 12499396 (Hum Mol Genet 2003, 12(2):155-167) is a pre-genomics wet-lab molecular-cell-biology paper: the ARHGEF6 (alphaPIX) - PARVB (beta-parvin) protein-protein interaction, its confirmation, the direct binding, the subcellular co-localization, the abolition of binding by two XLMR mutations, the differential effect on ARHGEF6-ARHGEF7 heterodimerization, and the integrin/fibronectin-adhesion link are ALL shown by manual wet-lab assays (yeast two-hybrid, co-immunoprecipitation in COS cells, GST pull-down, immunofluorescence microscopy, site-directed mutagenesis, cell-adhesion assay). There is NO bioinformatic pipeline, no high-throughput dataset, no count matrix, no code repository, and no specific computational value to regenerate, so nothing is in scope to reproduce (BRIEF rule 2). The paper is described well enough to understand fully but is not a computational study, hence not computationally reproducible. The only data it relies on are four open GenBank cDNA/mRNA reference records used for molecular cloning: AF207831 (ARHGEF6, 5'UTR+partial cds, 1213 bp), AF237769 (PARVB, complete cds, 1670 bp), D25304 (KIAA0006, 4804 bp), D63476 (KIAA0142, 5032 bp). All four were re-verified to resolve via NCBI esummary on 2026-06-22 (Homo sapiens mRNA, titles + lengths match) and are fully profiled in data/dataset_profile.json. NOT attempted: the wet-lab experiments (out of scope, not computationally reproducible). No result was forced or fabricated. This is a well-founded, healthy drop; a human reviewer should confirm the non_pipeline classification.
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
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
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v1 current initial assessmentassessed: 2026-06-19 ⛓ 9657539bc35b
✎ 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
- 2026-06-22
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-19no 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.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope analysis — PMID 12499396
Title: Interaction of alphaPIX (ARHGEF6) with beta-parvin (PARVB) suggests an involvement of alphaPIX in integrin-mediated signaling. Journal: Human Molecular Genetics 12(2):155-167, 2003-01-15. DOI/PMCID: none listed in brief; open abstract on PubMed.
What the paper actually does
A protein–protein interaction / cell-biology study of the X-linked mental retardation GEF alphaPIX (ARHGEF6) and its newly identified binding partner beta-parvin (PARVB). All reported results are generated by wet-lab assays:
| Result (paper) | Technique | Pipeline-derived? |
|---|---|---|
| alphaPIX–PARVB interaction discovered | Yeast two-hybrid screen | No — wet-lab |
| Interaction confirmed in mammalian cells | Co-immunoprecipitation (COS cells) | No — wet-lab |
| Direct binding | GST pull-down | No — wet-lab |
| Subcellular co-localization | Immunofluorescence microscopy | No — wet-lab/manual |
| Two XLMR mutations abolish PARVB binding | Mutagenesis + co-IP/pull-down | No — wet-lab |
| Differential effect on ARHGEF6–ARHGEF7 heterodimerization | Co-IP | No — wet-lab |
| Integrin/fibronectin-adhesion involvement | Cell-adhesion assay | No — wet-lab |
Bioinformatic / pipeline-derived results
None. The paper reports no sequencing run, no count matrix, no alignment, no differential-expression / clustering / variant-calling / imaging-ML output — nothing produced by a computational pipeline. There is no code link and no high-throughput data deposit.
Data the paper relies on
Four GenBank cDNA/mRNA sequence accessions used as the molecular-cloning reference for the genes studied (not analysis outputs):
- AF207831 — ARHGEF6 (alphaPIX) mRNA, 5'UTR + partial cds (1213 bp)
- AF237769 — beta-parvin (PARVB) mRNA, complete cds (1670 bp)
- D25304 — KIAA0006 mRNA (4804 bp)
- D63476 — KIAA0142 mRNA (5032 bp)
These are open, single-record reference sequences — used to design constructs,
not to derive a computational result. They are profiled in
data/dataset_profile.json.
Verdict
DROP — non_pipeline. There is no pipeline-derived computational result in
scope to reproduce. Every reported finding is a manual wet-lab experiment
(yeast two-hybrid, co-IP, GST pull-down, immunofluorescence, adhesion assay),
which is explicitly out of scope per BRIEF rule 2. No fabrication concern: the
paper never claims a computational output. No «our HPC» compute is warranted.
This is a well-founded drop (the outcome was correctly determined), not a failure of our infrastructure.
No individual results have been recorded for this entry yet.
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.
PMID 12499396 is a 2003 wet-lab protein-interaction paper (Hum Mol Genet 12:155-167) with no computational pipeline, dataset, or code — the ARHGEF6-PARVB interaction and its disruption by two XLMR mutations are shown only by yeast two-hybrid, co-IP, GST pull-down, immunofluorescence and adhesion assays. This is a well-founded non_pipeline drop, not an infrastructure failure or authors' defect: q1/q2 are red because no comparable computational input/endpoint exists, but q5/q7 stay yellow (out-of-scope, no fabrication signal) and severity is green because nothing was computed and no discrepancy exists. The four GenBank cloning references all resolve openly (verified 2026-06-20), confirming the cited sequences are intact.
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.