Journal of Open Source Science
Menu

pmid:28529692 Public

https://scm.piranha.sh/git/ada56728063306072cb24f17/sci-pmid-28529692 · at e589efb232b2

Download .sci Sign in to fork

Abnormal expression of ATP1A1 and ATP1A2 in breast cancer

pmid:28529692 · revision 7 · F1000Research

Original
2017
Created
2026-11-01
Ingested
2026-11-07
Paper record The research question, publication details and source material recorded for this paper.

Breast cancer is the first in incidence and the second in death among all solid tumors occurring in women. The identification of molecular genetic abnormalities in breast cancer is important to improve the results of treatment. In the present study, we analyzed microarray data of breast cancer expression profiling (NCBI GEO database, accession GSE65194), focusing on Na +/K +-ATPase coding genes. We found overexpression of the ATP1A1 and down-regulation of the ATP1A2. We expect that our research could help to improve the understanding of predictive and prognostic features of breast cancer. Keywords: breast cancer, Na+/K+-ATPase, gene expression, abnormality, ATP1A1, ATP1A2

Alexey Bogdanov, Fedor Moiseenko, Michael Dubina

DOI
10.12688/f1000research.10481.1
PMID
28529692
Journal
F1000Research
Published
2017
Revision
7
Format version
1.5
Content hash
sha256:6b247969db794ceed01e4ee56a727d5280d1e500aa30400983782278456d9f7f

Recomputed from the file: it matches.

Opened from
pmid:28529692
Written
2026-11-01T11:44:20Z
Updated
2026-11-07T10:19:56Z
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

10.12688/f1000research.10481.1

https://doi.org/10.12688/f1000research.10481.1

xml · 8,810 bytes · sha256:b52c152ee6cd127bf20948915bce7ef4e8d743048657f0fe8c3441f877d98c57

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]#T1

jats-table · 583 bytes · sha256:afeba1f43a9ff6fbabd40311ddbef13ba564b2dafbcea3e2eb2ca82a3275cf6a

NKA genes expression in breast cancer samples relative to normal breast tissue.

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

CellLine
14
Healthy
11
Her2
39
Luminal A
29
Luminal B
30
TNBC
55

As the paper states them

Her2
30
Lum A
29
Lum B
30
TNBC
41
normal breast tissue
11

141 samples in total.

Reference group: normal breast tissue.

Array data for 41 triple negative samples (TNBC group), 30 Her2-positive (Her2 group), 30 Luminal B (Lum B group), 29 Luminal A (Lum A group) breast cancer samples and 11 normal breast tissue samples were investigated.

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

In GSE65194 Affymetrix microarray data analyzed by one-way between-subjects ANOVA, ATP1A1 was overexpressed approximately 1.5-fold in all breast cancer groups (p<0.05), while ATP1A2 expression decreased by more than 2-fold (p<0.05).

  1. 1

    Read the published estimate from the source

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

    in: source:pmid:28529692

    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:GSE65194

    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:GSE65194

    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
RMA
steps
background correction, probe set signal integration, quantile normalization
software
Expression Console 1.4
normalisation_cohort
not stated

operations still missing: microarray_rma_normalise

Preanalytical procedures consisted of a robust multichip analysis (RMA) algorithm 21, including background correction, probe set signal integration, and quantile normalization. For this purpose, we used Expression Console 1.4 software (Affymetrix, Inc. USA).

One-way analysis of variance

expressible

one-way between subjects ANOVA

alpha
0.05
design
one-way between subjects
software
Transcriptome Analysis Console 3.0
We utilized Transcriptome Analysis Console 3.0 software (Affymetrix, Inc. USA) to analyze the obtained CHP files and to detect differentially expressed genes using one-way between subjects ANOVA.

Group comparison against a reference group

not expressible

expression relative to a reference group

reference_group
normal breast tissue
scale
not stated

operations still missing: group_relative_expression

NKA genes expression in breast cancer samples relative to normal breast tissue.
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 prose target: ATP1A1 overexpressed approximately 1.5 times in every breast cancer group, p<0.05.

 group_comparison_anova 1.5 fold change (ATP1A1) complete

claim-target-result

Published significance threshold: p<0.05.

 group_comparison_anova 0.05 exclusive p-value threshold complete

claim-target-result

Table 1, ATP1A1, Lum A; ANOVA p-value 0.009016; source cell '1.53 (0.009016)'.

 group_comparison_anova 1.53 relative expression fold change complete

claim-target-result

Table 1, ATP1A1, Lum A; source cell '1.53 (0.009016)'.

 group_comparison_anova 0.009016 ANOVA p-value complete

claim-target-result

Table 1, ATP1A1, Lum B; ANOVA p-value 0.04454; source cell '1.38 (0.04454)'.

 group_comparison_anova 1.38 relative expression fold change complete

claim-target-result

Table 1, ATP1A1, Lum B; source cell '1.38 (0.04454)'.

 group_comparison_anova 0.04454 ANOVA p-value complete

claim-target-result

Table 1, ATP1A1, Her2; ANOVA p-value 0.005926; source cell '1.66 (0.005926)'.

 group_comparison_anova 1.66 relative expression fold change complete

claim-target-result

Table 1, ATP1A1, Her2; source cell '1.66 (0.005926)'.

 group_comparison_anova 0.005926 ANOVA p-value complete

claim-target-result

Table 1, ATP1A1, TNBC; ANOVA p-value 0.015725; source cell '1.44 (0.015725)'.

 group_comparison_anova 1.44 relative expression fold change complete

claim-target-result

Table 1, ATP1A1, TNBC; source cell '1.44 (0.015725)'.

 group_comparison_anova 0.015725 ANOVA p-value complete

claim-target-result

Table 1, ATP1A2, Lum A; ANOVA p-value 1.85e-07; source cell '-2.49 (1.85e-07)'.

 group_comparison_anova -2.49 relative expression fold change complete

claim-target-result

Table 1, ATP1A2, Lum A; source cell '-2.49 (1.85e-07)'.

 group_comparison_anova 1.85E-7 ANOVA p-value complete

claim-target-result

Table 1, ATP1A2, Lum B; ANOVA p-value 8.50e-09; source cell '-2.52 (8.50e-09)'.

 group_comparison_anova -2.52 relative expression fold change complete

claim-target-result

Table 1, ATP1A2, Lum B; source cell '-2.52 (8.50e-09)'.

 group_comparison_anova 8.5E-9 ANOVA p-value complete

claim-target-result

Table 1, ATP1A2, Her2; ANOVA p-value 5.48e-08; source cell '-2.78 (5.48e-08)'.

 group_comparison_anova -2.78 relative expression fold change complete

claim-target-result

Table 1, ATP1A2, Her2; source cell '-2.78 (5.48e-08)'.

 group_comparison_anova 5.48E-8 ANOVA p-value complete

claim-target-result

Table 1, ATP1A2, TNBC; ANOVA p-value 2.08e-11; source cell '-2.87 (2.08e-11)'.

 group_comparison_anova -2.87 relative expression fold change complete

claim-target-result

Table 1, ATP1A2, TNBC; source cell '-2.87 (2.08e-11)'.

 group_comparison_anova 2.08E-11 ANOVA p-value complete

claim-target-result

Table 1, ATP1A3, Lum A; ANOVA p-value 0.429089; source cell '-1.05 (0.429089)'.

 group_comparison_anova -1.05 relative expression fold change complete

claim-target-result

Table 1, ATP1A3, Lum A; source cell '-1.05 (0.429089)'.

 group_comparison_anova 0.429089 ANOVA p-value complete

claim-target-result

Table 1, ATP1A3, Lum B; ANOVA p-value 0.308298; source cell '1.03 (0.308298)'.

 group_comparison_anova 1.03 relative expression fold change complete

claim-target-result

Table 1, ATP1A3, Lum B; source cell '1.03 (0.308298)'.

 group_comparison_anova 0.308298 ANOVA p-value complete

claim-target-result

Table 1, ATP1A3, Her2; ANOVA p-value 0.768041; source cell '-1.04 (0.768041)'.

 group_comparison_anova -1.04 relative expression fold change complete

claim-target-result

Table 1, ATP1A3, Her2; source cell '-1.04 (0.768041)'.

 group_comparison_anova 0.768041 ANOVA p-value complete

claim-target-result

Table 1, ATP1A3, TNBC; ANOVA p-value 0.527878; source cell '-1.04 (0.527878)'.

 group_comparison_anova -1.04 relative expression fold change complete

claim-target-result

Table 1, ATP1A3, TNBC; source cell '-1.04 (0.527878)'.

 group_comparison_anova 0.527878 ANOVA p-value 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

treatment. In the present study, we analyzed microarray data of breast cancer expression profiling (

group_comparison

partial

assay:2 · analysis · version f2132e96ae6c7a4e

needs: group_comparison_anova, microarray_rma_normalise, group_relative_expression

We utilized Transcriptome Analysis Console 3.0 software (Affymetrix, Inc. USA) to analyze the obtained CHP files and to detect differentially expressed genes using one-way between subjects ANOVA.
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

Still to build

  • microarray_rma_normalise
  • group_relative_expression

method

The DSL catalogue has no operation for: microarray_rma_normalise, group_relative_expression.

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:GSE65194 licence not read
  • asset:data:geo:GSE65194 not downloaded
  • data.group_sizes_conflict
  • data.sample_set_unresolved
  • execution.not_run
  • method.microarray_rma_normalise
  • method.multiple_testing_not_stated
  • review.human_critique
  • review.independent_reader
  • review.machine_critique
  • step:run_analysis blocked on method:microarray_rma_normalise
  • target.relative_expression_scale_undefined

experiment

  • step:run_analysis blocked on method:microarray_rma_normalise

data

  • asset:data:geo:GSE65194 licence not read
  • asset:data:geo:GSE65194 not downloaded
  • data.group_sizes_conflict
  • data.sample_set_unresolved

analysis

  • method.microarray_rma_normalise
  • method.multiple_testing_not_stated
  • target.relative_expression_scale_undefined

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:28529692:abnormal-expression-of-atp1a1-and-atp1a2-in-breast-cancer-30ee8f18 revision 8 · 3 commits Published

Files

pmid:28529692.json 38,964 bytes