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pmid:35280505

Biomarkers for Breast Adenocarcinoma Using In Silico Approaches.

Jhansi Pandi · Ajucarmelprecilla Arulprakasam · Ranjithkumar Dhandapani · Saikishore Ramanathan · Sathiamoorthi Thangavelu · Jayaprakash Chinnappan · V Vidhya Rajalakshmi · Saad Alghamdi · Nashwa Talaat Shesha · S Prasath

Evidence-based complementary and alternative medicine : eCAM · 2022 doi:10.1155/2022/7825272

Paper

complete

Experiment

complete

Data

partial

Analysis

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Execution

absent

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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pmid:35280505
kind
science-record
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sha256:aebb715a5ddaad2bc556671609d4b5bc18c88b186b0e2360f6f09780c478a3e4
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created_at
2026-11-01T18:14:03Z
updated_at
2026-11-01T22:48:39Z
generator object · 2 fields
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paper object · 10 fields
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title
Biomarkers for Breast Adenocarcinoma Using In Silico Approaches.
doi
10.1155/2022/7825272
pmid
35280505
authors array · 10 items
[0]
Jhansi Pandi
[1]
Ajucarmelprecilla Arulprakasam
[2]
Ranjithkumar Dhandapani
[3]
Saikishore Ramanathan
[4]
Sathiamoorthi Thangavelu
[5]
Jayaprakash Chinnappan
[6]
V Vidhya Rajalakshmi
[7]
Saad Alghamdi
[8]
Nashwa Talaat Shesha
[9]
S Prasath
journal
Evidence-based complementary and alternative medicine : eCAM
year
2022
abstract
This work elucidates the idea of finding probable critical genes linked to breast adenocarcinoma. In this study, the GEO database gene expression profile data set (GSE70951) was retrieved to look for genes that were expressed variably across breast adenocarcinoma samples and healthy tissue samples. The genes were confirmed to be part of the PPI network for breast cancer pathogenesis and prognosis. In Cytoscape, the CytoHubba module was used to discover the hub genes. For correlation analysis, the predictive biomarker of these hub genes, as well as GEPIA, was used. A total of 155 (85 upregulated genes and 70 downregulated genes) were identified. By integrating the PPI and CytoHubba data, the major key/hub genes were selected from the results. The KM plotter is employed to find the prognosis of those major pivot genes, and the outcome shows worse prognosis in breast adenocarcinoma patients. Further experimental validation will show the predicted expression levels of those hub genes. The overall result of our study gives the consequences for the identification of a critical gene to ease the molecular targeting therapy for breast adenocarcinoma. It could be used as a prognostic biomarker and could lead to therapy options for breast adenocarcinoma.
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In breast cancer, the Kaplan–Meier plotter was used to investigate the prognostic benefits of every single pivot gene.
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sections[6] "2.4. Survival Analysis of Hub Genes" paragraph 2
quote
In breast cancer, the Kaplan–Meier plotter was used to investigate the prognostic benefits of every single pivot gene.
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The data used to support the findings of this study are available from the corresponding author upon request.
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In this study, these 10 hub genes show a worse survival rate in overall and confirm the prognostic value of BAC (Figure 7).
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sections[12] "3.4. Overall Survival for Key Genes" paragraph 2
quote
In this study, these 10 hub genes show a worse survival rate in overall and confirm the prognostic value of BAC (Figure 7).
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In this study, these 10 hub genes show a worse survival rate in overall and confirm the prognostic value of BAC (Figure 7).
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Paired Breast Adenocarcinoma and Adjacent Normal tissue
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In breast cancer, the Kaplan–Meier plotter was used to investigate the prognostic benefits of every single pivot gene.
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ppi_network
label
Network / pathway analysis
dsl_operations array · 3 items
[0]
build_graph
[1]
centrality_scores
[2]
pathway_enrich
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
edge_list
evidence object · 3 fields
score
0.7
band
medium
quote
PPI
targets array · 0 items
gaps array · 0 items
capability object · 3 fields
state
complete
requirements array · 1 item
[0] object · 6 fields
capability_id
capability:computational_analysis
label
Computational analysis platform
assay_families array · 9 items
[0]
meta_analysis
[1]
machine_learning
[2]
survival_analysis
[3]
statistical_regression
[4]
pca
[5]
molecular_docking
[6]
network_analysis
[7]
differential_expression
[8]
gwas
candidate
Automated Assays Laravel application and simulated adapters
gaps array · 0 items
readiness object · 8 fields
state
complete
tier
R1
blocked_on
nothing:replicable_now
axes object · 3 fields
method object · 5 fields
tier
R1
expressible
true
required_operations array · 1 item
[0]
survival_km
missing_operations array · 0 items
basis
The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier.
capability object · 4 fields
tier
R1
capability_id
capability:computational_analysis
availability_state
owned
basis
The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here.
data object · 6 fields
tier
R1
reachable
true
accessions array · 1 item
[0]
GSE70951
resolved_accessions array · 1 item
[0]
GSE70951
statements array · 1 item
[0]
The data used to support the findings of this study are available from the corresponding author upon request.
basis
The paper names GSE70951 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 1 item
[0]
survival_km
assets array · 2 items
[0]
source:pmid:35280505
[1]
data:geo:GSE70951
steps array · 1 item
[0]
run_analysis
must_build object · 5 fields
dsl_operations array · 0 items
converters array · 0 items
readers array · 0 items
capabilities array · 0 items
data_gaps array · 1 item
[0]
data:geo:GSE70951
gaps array · 0 items
review object · 5 fields
state
partial
machine_critique object · 5 fields
kind
extraction_review
reader object · 5 fields
model
MiniMax-M3.1-Flash
provider
minimax
provider_family
minimax
read_at
2026-11-01T17:37:39Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
5
usage object · 3 fields
prompt_tokens
7281
completion_tokens
2034
cached_tokens
264
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
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minimax
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review.independent_reader
[1]
review.machine_critique
[2]
review.human_critique
execution object · 5 fields
state
absent
status
not_run
mode
null
runs array · 0 items
gaps array · 1 item
[0]
execution.not_run
provenance object · 7 fields
entities array · 3 items
[0] object · 3 fields
id
pmid:35280505
type
paper
label
pmid:35280505
[1] object · 3 fields
id
source:pmid:35280505
type
manuscript
label
PMID 35280505 full text
[2] object · 3 fields
id
data:geo:GSE70951
type
dataset
label
GEO GSE70951
activities array · 3 items
[0] object · 4 fields
id
activity-reading-sci-2026-11-01
type
classification
used array · 3 items
[0] object · 3 fields
id
pmid:35280505
type
paper
label
pmid:35280505
[1] object · 3 fields
id
source:pmid:35280505
type
manuscript
label
PMID 35280505 full text
[2] object · 3 fields
id
data:geo:GSE70951
type
dataset
label
GEO GSE70951
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-35280505
type
extraction
used array · 1 item
[0]
source:pmid:35280505
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE70951
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE70951
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
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Corpus assay engine
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id
agent:minimax-reader
type
software
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MiniMax literature reader
source_run_id
reading-sci-2026-11-01
dsl_catalogue_fingerprint
343fb30756ba6ec3
capability_table_fingerprint
2cb3e42f047d2ecf
snapshot_id
ba34b49490d9bfaf
lineage object · 4 fields
parent_id
pmid:35280505
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sha256:bd438949590d4edec2ec7cdafc793ce5f563b73ca6a9321815f82ed236e99fb0
fork_of
null
gaps array · 6 items
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asset:data:geo:GSE70951 licence not read
[1]
asset:data:geo:GSE70951 not downloaded
[2]
execution.not_run
[3]
review.human_critique
[4]
review.independent_reader
[5]
review.machine_critique
assays array · 1 item
[0] object · 11 fields
role
analysis
definition_id
survival_analysis
definition_version
f2132e96ae6c7a4e
required_operations array · 1 item
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survival_km
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
In breast cancer, the Kaplan–Meier plotter was used to investigate the prognostic benefits of every single pivot gene.
order_basis
analysis_only
id
assay:1
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35280505", "kind": "science-record", "revision": 5, "content_hash": "sha256:aebb715a5ddaad2bc556671609d4b5bc18c88b186b0e2360f6f09780c478a3e4", "created_at": "2026-11-01T18:14:03Z", "updated_at": "2026-11-01T22:48:39Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Biomarkers for Breast Adenocarcinoma Using In Silico Approaches.", "doi": "10.1155/2022/7825272", "pmid": "35280505", "authors": ["Jhansi Pandi", "Ajucarmelprecilla Arulprakasam", "Ranjithkumar Dhandapani", "Saikishore Ramanathan", "Sathiamoorthi Thangavelu", "Jayaprakash Chinnappan", "V Vidhya Rajalakshmi", "Saad Alghamdi", "Nashwa Talaat Shesha", "S Prasath"], "journal": "Evidence-based complementary and alternative medicine : eCAM", "year": 2022, "abstract": "This work elucidates the idea of finding probable critical genes linked to breast adenocarcinoma. In this study, the GEO database gene expression profile data set (GSE70951) was retrieved to look for genes that were expressed variably across breast adenocarcinoma samples and healthy tissue samples. The genes were confirmed to be part of the PPI network for breast cancer pathogenesis and prognosis. In Cytoscape, the CytoHubba module was used to discover the hub genes. For correlation analysis, the predictive biomarker of these hub genes, as well as GEPIA, was used. A total of 155 (85 upregulated genes and 70 downregulated genes) were identified. By integrating the PPI and CytoHubba data, the major key/hub genes were selected from the results. The KM plotter is employed to find the prognosis of those major pivot genes, and the outcome shows worse prognosis in breast adenocarcinoma patients. Further experimental validation will show the predicted expression levels of those hub genes. The overall result of our study gives the consequences for the identification of a critical gene to ease the molecular targeting therapy for breast adenocarcinoma. It could be used as a prognostic biomarker and could lead to therapy options for breast adenocarcinoma.", "claims": [{"id": "claim-method", "statement": "In breast cancer, the Kaplan–Meier plotter was used to investigate the prognostic benefits of every single pivot gene.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35280505", "locator": "sections[6] \"2.4. 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This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE70951"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {"hazard_ratio": "dence intervals for the hazard ratio"}, "inputs": ["data:geo:GSE70951"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35280505", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/7825272", 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