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Gene expression profiling of human calcific aortic valve disease

pmid:26981379 · revision 5 · 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
5
Format version
1.5
Content hash
sha256:8342463b7805c703875c2460bba031572d37951e55b21b653cd26022f9e29bbf

Recomputed from the file: it matches.

Opened from
pmid:26981379
Written
2026-11-01T11:44:19Z
Updated
2026-11-03T11:53:22Z
Made by
Corpus assay engine, MiniMax literature reader
Source run
pilot-sci-2026-11-01
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

fibro(sclero)tic valves
5
non-calcified control
5
stenotic valves
5

15 samples in total.

Samples are from 3 groups: non-calcified control, fibro(sclero)tic and stenotic valves, n = 5 in each group

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

    Read the published estimate from the source

    The claim, method and evidence span published with the source article.

    in: source:pmid:26981379

    out: the published estimate and its evidence

    complete

    other

  2. 2

    Obtain the source data from the named repository

    The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.

    in: data:geo:GSE51472

    out: the source data with its repository provenance

    complete

    data-preparation

  3. 3

    Run the published analysis

    Apply the paper's statistical method to the resolved series and compare the result with the published target.

    in: data:geo:GSE51472

    out: the replicated result and its comparison

    blocked on method:microarray_rma_normalise

    blocked

    analysis

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

Microarray preprocessing

not expressible

robust multiarray average normalisation

algorithm
Robust Multi-Array Average (RMA)
input
Affymetrix CEL files generated by GCOS 1.2
software
GeneSpring version 7.2 (Agilent)
cohort_normalisation
all the samples were then normalized to the median of the controls
normalisation_cohort
the controls: the non-calcified control group, n = 5, named by the paper's own group list

operations still missing: microarray_rma_normalise

CEL files (from GCOS 1.2) were imported into GeneSpring using the Robust Multi-Array Average normalization. All the samples were then normalized to the median of the controls.

One-way analysis of variance

expressible

one-way ANOVA with Benjamini and Hochberg false discovery rate

alpha
0.05
fold_change_threshold
2
false_discovery_rate
Benjamini-Hochberg
Genes were defined as differentially expressed if the change was at least 2.0-fold and statistically significant (P < 0.05, one-way ANOVA and Benjamini and Hochberg false discovery rate).
The numbers to reproduce The values the paper prints, with the tolerance each one is held to.
Claim Operation Expected Tolerance State

claim-target-result

Published selection threshold: at least 2.0-fold. This is a threshold, not an effect estimate.

 differential_expression_fit 2 fold-change threshold complete

claim-target-result

Published significance threshold: P < 0.05.

 group_comparison_anova 0.05 exclusive p-value threshold complete
The assays in this file Each assay the file names, with the operations it needs and the definition it was read from.

microarray

partial

assay:1 · data_generation · version 99e1195c7d6f

ocessing and statistical analysis of the DNA microarray data is provided in this article. Interpreta

group_comparison

partial

assay:2 · analysis · version f2132e96ae6c7a4e

needs: group_comparison_anova, fdr_bh, microarray_rma_normalise

Genes were defined as differentially expressed if the change was at least 2.0-fold and statistically significant (P < 0.05, one-way ANOVA and Benjamini and Hochberg false discovery rate).
Can this run here What the file says about running this experiment, and what still stands in the way.
State
blocked · tier R4
Blocked on
method:microarray_rma_normalise

can run: group_comparison_anova, fdr_bh

Still to build

  • microarray_rma_normalise

method

The DSL catalogue has no operation for: microarray_rma_normalise.

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

Runs

Nothing has run against this file

The file records no execution. It is the paper's own definition of its experiment, read and held by the journal.

Review carried by the file

partial

Reader
MiniMax-M3.1-Flash (minimax)
Calls
5

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.
  • asset:data:geo:GSE51472 licence not read
  • asset:data:geo:GSE51472 not downloaded
  • execution.not_run
  • method.microarray_rma_normalise
  • review.human_critique
  • review.independent_reader
  • review.machine_critique
  • step:run_analysis blocked on method:microarray_rma_normalise

experiment

  • step:run_analysis blocked on method:microarray_rma_normalise

data

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

analysis

  • method.microarray_rma_normalise

readiness

  • method:microarray_rma_normalise

review

  • review.independent_reader
  • review.machine_critique
  • review.human_critique

execution

  • execution.not_run
Forks opened from this paper Each fork is a repository of its own, with the paper it was opened from.
fork:pmid:26981379:gene-expression-profiling-of-human-calcific-aortic-valve-disease-8db11e48 revision 22 · 3 commits Published

Files

pmid:26981379.json 28,745 bytes