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https://scm.piranha.sh/git/ada56728063306072cb24f17/sci-fork-pmid-26981379-gene-expression-profiling-of-human-calcific-aortic-valve-disease-8db11e48 · at 0d46d2c56df8

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Gene expression profiling of human calcific aortic valve disease

fork:pmid:26981379:gene-expression-profiling-of-human-calcific-aortic-valve-disease-8db11e48 · revision 22 · Genomics Data

Original
2015
Created
2026-11-01
Ingested
2026-11-07
Paper record The research question, publication details and source material recorded for this paper.

Calcific aortic valve disease is a slowly progressive disorder that ranges from mild valve thickening (i.e. aortic sclerosis) to severe calcification of valves (i.e. aortic stenosis). Gene expression profiling analysis of non-calcified controls, sclerotic, and calcified aortic valves was performed to better understand the progression of calcific aortic valve disease. The complementary information related to processing and statistical analysis of the DNA microarray data is provided in this article. Interpretation of this data can be found in a research article entitled “MicroRNA-125b and chemokine CCL4 expression are associated with calcific aortic valve disease” [1]. The microarray data complies with MIAME guidelines and is deposited in the Gene Expression Omnibus (GEO) database under accession number GSE51472.

Jaana Rysä

DOI
10.1016/j.gdata.2015.12.015
PMID
26981379
Journal
Genomics Data
Published
2015
Revision
22
Format version
1.2
Content hash
sha256:71f971a55237fe178b6a50c6fc30b94dfacd30914972e4e0b4ef2a774298a996

Recomputed from the file: it matches.

Opened from
fork:pmid:26981379:gene-expression-profiling-of-human-calcific-aortic-valve-disease-8db11e48
Fork of pmid:26981379
Written
2026-11-01T16:10:49.000000Z
Updated
2026-11-03T08:03:44.105145Z
Made by
Automated Assays Administrator, Automated Assays
Source run
assays-session-8db11e48-2149-4d81-b70c-0b751de5f0f5
Data sources The sources the file names, with the access and the state the file records for each one.

manuscript · open · resolved

10.1016/j.gdata.2015.12.015

https://doi.org/10.1016/j.gdata.2015.12.015

xml · 4,822 bytes · sha256:124d509483f99c4a153b876f5736a3e5627805190e742563ebfe58736dbd5a9c

Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.

table · open · verified

section[1]/table-wrap[1]#t0005

jats-table · 791 bytes · sha256:899445f8a1682cc33fee2cc9dd59a6c66ab864e9975cfe0b1e3e9da343876edd

The samples analysed The group sizes the file holds, and the group sizes the paper itself states. A run is only comparable when it used the same cohort.

In this file

Calcified aortic valve
5
Normal aortic valve
5
Sclerotic aortic valve
5

As the paper states them

Reproducibility map Follow the research stages and see which inputs each stage needs and what state the file records for it.

The study identified differentially expressed genes using a ≥2.0-fold change with one-way ANOVA and Benjamini–Hochberg false discovery rate (P < 0.05), and the source microarray data were deposited in GEO under accession number GSE51472.

  1. 1

    Validate the dataset schema and hash it

    complete

    computational

  2. 2

    Confirm at least two groups with at least two observations each

    complete

    computational

  3. 3

    Compute per-group descriptives

    complete

    computational

  4. 4

    Test variance homogeneity and screen each group for normality

    complete

    computational

  5. 5

    Run the one-way analysis of variance

    complete

    computational

  6. 6

    Compare every pair of groups and correct across the pairs

    complete

    computational

  7. 7

    Package the result and its hashes

    complete

    computational

The methods the paper publishes Each method as the paper states it, with the evidence the file holds for it.

Group comparison analysis

expressible

group_comparison_anova

alpha
{"type":"number","description":"The significance level, declared before the run and recorded with the result.","default":0.05}
Compare a continuous measurement across two or more groups with a one-way analysis of variance, report the assumption checks the test depends on, and compare every pair of groups with Welch's unequal-variance t statistic under Holm's correction.
The assays in this file Each assay the file names, with the operations it needs and the definition it was read from.

group-comparison-analysis

supported

assay:1 · primary · version 0.1.0

needs: group_comparison_wilcoxon, group_comparison_mann_whitney, student_t, group_comparison_anova

sha256:f1c5d3dfb8ca3c3061030d0f366addd1f61dd994520aa65a406632940618b75a

Can this run here What the file says about running this experiment, and what still stands in the way.
State
complete · tier R1
Blocked on
nothing:replicable_now

can run: group_comparison_anova, fdr_bh

method

The named method is represented in the DSL catalogue.

capability

The corpus capability table owns computational analysis.

data

The GEO series resolves and its sample accessions are listed. No dataset was downloaded and no licence was read.

The result run What has run against this file, and the review the file carries.

Runs

2f3bceb6-55ca-44fe-bc02-75359983f659

group_comparison_anova · complete

ran against
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group_comparison_anova · complete

ran against
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version
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f1e49f32-4439-4053-931f-3f0b2a868254

group_comparison_anova · complete

ran against
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version
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provider
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evidence
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published_figure_reconciliation · refused

ran against
pmid:26981379
version
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provider
automated-assays-computational

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published_figure_reconciliation · refused

ran against
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version
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provider
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published_figure_reconciliation · refused

ran against
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version
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provider
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group_comparison_anova · complete

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provider
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result
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evidence
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evidence
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group_comparison_anova · complete

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provider
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evidence
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Review carried by the file

absent

No person has reviewed this file. The reader's assessment is an opinion and not a decision.

Scope and limitations What this file does not cover, as the file itself states it.
  • execution.unbound: 3 runs against this record are not bound to a version of it, so are not published as evidence on an assay entry.

data

  • asset:data:geo:GSE51472 not downloaded
  • asset:data:geo:GSE51472 licence not read

review

  • review.absent: this document is a working version. Review and publication are separate actions, and they belong to the Journal.
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