Corpus Engine Towards a reproducible .science file.
← All .science files

pmid:33469842

CHRNA5 belongs to the secondary estrogen signaling network exhibiting prognostic significance in breast cancer.

Huma Shehwana · Ayse G Keskus · Sila E Ozdemir · Azer A Acikgöz · Rumeysa Biyik-Sit · Ilgin Cagnan · Damla Gunes · Ermira Jahja · Sahika Cingir-Koker · Gizem Olmezer · Ceren Sucularli · Ozlen Konu

Cellular oncology (Dordrecht, Netherlands) · 2021 doi:10.1007/s13402-020-00581-x

Paper

complete

Experiment

complete

Data

partial

Analysis

partial

Execution

absent

Execution evidence has not yet been added to this .science file. Explore its methods, data and open questions to plan the next step.
Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
id
pmid:33469842
kind
science-record
content_hash
sha256:10d363c0fa9f703546e1c495535401e3e2dfcff97c2b49ed876b84fc21730fda
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T17:34:38Z
updated_at
2026-11-01T21:24:33Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
CHRNA5 belongs to the secondary estrogen signaling network exhibiting prognostic significance in breast cancer.
doi
10.1007/s13402-020-00581-x
pmid
33469842
authors array · 12 items
[0]
Huma Shehwana
[1]
Ayse G Keskus
[2]
Sila E Ozdemir
[3]
Azer A Acikgöz
[4]
Rumeysa Biyik-Sit
[5]
Ilgin Cagnan
[6]
Damla Gunes
[7]
Ermira Jahja
[8]
Sahika Cingir-Koker
[9]
Gizem Olmezer
[10]
Ceren Sucularli
[11]
Ozlen Konu
journal
Cellular oncology (Dordrecht, Netherlands)
year
2021
abstract
PURPOSE: Cholinergic signals can be important modulators of cellular signaling in cancer. We recently have shown that knockdown of nicotinic acetylcholine receptor subunit alpha 5, CHRNA5, diminishes the proliferative potential of breast cancer cells. However, modulation of CHRNA5 expression in the context of estrogen signaling and its prognostic implications in breast cancer remained unexplored. METHODS: Meta-analyses of large breast cancer microarray cohorts were used to evaluate the association of CHRNA5 expression with estrogen (E2) treatment, estrogen receptor (ER) status and patient prognosis. The results were validated through RT-qPCR analyses of multiple E2 treated cell lines, CHRNA5 depleted MCF7 cells and across a breast cancer patient cDNA panel. We also calculated a predicted secondary (PS) score representing direct/indirect induction of gene expression by E2 based on a public dataset (GSE8597). Co-expression analysis was performed using a weighted gene co-expression network analysis (WGCNA) pipeline. Multiple other publicly available datasets such as CCLE, COSMIC and TCGA were also analyzed. RESULTS: Herein we found that CHRNA5 expression was induced by E2 in a dose- and time-dependent manner in breast cancer cell lines. ER- breast tumors exhibited higher CHRNA5 expression levels than ER+ tumors. Independent meta-analysis for survival outcome revealed that higher CHRNA5 expression was associated with a worse prognosis in untreated breast cancer patients. Furthermore, CHRNA5 and its co-expressed gene network emerged as secondarily induced targets of E2 stimulation. These targets were largely downregulated by exposure to CHRNA5 siRNA in MCF7 cells while the response of primary ESR1 targets was dependent on the direction of the PS-score. Moreover, primary and secondary target genes were uncoupled and clustered distinctly based on multiple public datasets. CONCLUSION: Our findings strongly associate increased expression of CHRNA5 and its co-expression network with secondary E2 signaling and a worse prognosis in breast cancer.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
Independent meta-analysis for survival outcome revealed that higher CHRNA5 expression was associated with a worse prognosis in untreated breast cancer patients. Co-expression analysis was performed using a weighted gene co-expression network analysis (WGCNA) pipeline.
kind
methodological
target
null
evidence array · 2 items
[0] object · 3 fields
asset
source:pmid:33469842
locator
sections[0] "Abstract" paragraph 3
quote
Independent meta-analysis for survival outcome revealed that higher CHRNA5 expression was associated with a worse prognosis in untreated breast cancer patients.
[1] object · 3 fields
asset
source:pmid:33469842
locator
sections[0] "Abstract" paragraph 2
quote
Co-expression analysis was performed using a weighted gene co-expression network analysis (WGCNA) pipeline.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
We also calculated a predicted secondary (PS) score representing direct/indirect induction of gene expression by E2 based on a public dataset (GSE8597).
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:33469842
locator
sections[0] "Abstract" paragraph 2
quote
We also calculated a predicted secondary (PS) score representing direct/indirect induction of gene expression by E2 based on a public dataset (GSE8597).
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
steps array · 3 items
[0] object · 13 fields
id
read_published_estimate
order
1
name
Read the published estimate from the source
kind
other
state
complete
blocked_on
null
description
The claim, method and evidence span published with the source article.
parameters object · 0 fields
inputs array · 1 item
[0]
source:pmid:33469842
outputs array · 1 item
[0]
the published estimate and its evidence
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
id
obtain_source_data
order
2
name
Obtain the source data from the named repository
kind
data-preparation
state
complete
blocked_on
null
description
The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE8597
outputs array · 1 item
[0]
the source data with its repository provenance
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
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.
parameters object · 0 fields
inputs array · 1 item
[0]
data:geo:GSE8597
outputs array · 1 item
[0]
the replicated result and its comparison
instruments array · 0 items
reagents array · 0 items
materials array · 0 items
instruments array · 0 items
reagents array · 0 items
conditions object · 0 fields
gaps array · 0 items
data object · 3 fields
state
partial
assets array · 2 items
[0] object · 15 fields
id
source:pmid:33469842
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1007/s13402-020-00581-x
sha256
sha256:7282181eaa198528984bdf3a5315ccc8eb60d9fbd4af2250074df8902fb8b91a
bytes
2136
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1007/s13402-020-00581-x
version
null
note
Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.
structure object · 4 fields
pmcid
PMC12980715
source
ncbi_pmc_fulltext
coverage
whole_body
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE8597
role
raw
format
geo-series
media_type
application/vnd.ncbi.geo-series+json
uri
https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE8597
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE8597
version
null
note
We also calculated a predicted secondary (PS) score representing direct/indirect induction of gene expression by E2 based on a public dataset (GSE8597).
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
We also calculated a predicted secondary (PS) score representing direct/indirect induction of gene expression by E2 based on a public dataset (GSE8597).
access_statement_kind
repository_route_statement
sample_accessions array · 16 items
[0]
GSM213318
[1]
GSM213319
[2]
GSM213320
[3]
GSM213321
[4]
GSM213322
[5]
GSM213323
[6]
GSM213324
[7]
GSM213325
[8]
GSM213326
[9]
GSM213327
[10]
GSM213328
[11]
GSM213329
[12]
GSM213330
[13]
GSM213331
[14]
GSM213332
[15]
GSM213333
sample_count
16
group_sizes
null
group_sizes_basis
null
platform
570
taxon
Homo sapiens
title
Gene expression analysis of hormone treated MCF7 breast cancer cells in the presence or absence of cycloheximide
resolution_checked_at
2026-11-01T17:30:42Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE8597 not downloaded
[1]
asset:data:geo:GSE8597 licence not read
analysis object · 4 fields
state
partial
methods array · 1 item
[0] object · 10 fields
id
method-1
family
null
specific
null
label
Independent meta-analysis for survival outcome and weighted gene co-expression network analysis (WGCNA)
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
evidence object · 3 fields
score
1
band
reordered
quote
Independent meta-analysis for survival outcome revealed that higher CHRNA5 expression was associated with a worse prognosis in untreated breast cancer patients. Co-expression analysis was performed using a weighted gene co-expression network analysis (WGCNA) pipeline.
targets array · 0 items
gaps array · 1 item
[0]
method.reader_named_unmapped
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
blocked
tier
R4
blocking_axis
method
blocked_on
method:not_determinable
axes object · 3 fields
method object · 5 fields
tier
R4
expressible
false
required_operations array · 0 items
missing_operations array · 0 items
basis
The reader quoted the method the paper names (Independent meta-analysis for survival outcome and weighted gene co-expression network analysis (WGCNA)), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible.
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]
GSE8597
resolved_accessions array · 1 item
[0]
GSE8597
statements array · 1 item
[0]
We also calculated a predicted secondary (PS) score representing direct/indirect induction of gene expression by E2 based on a public dataset (GSE8597).
basis
The paper names GSE8597 in GSE8597 and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 0 items
assets array · 2 items
[0]
source:pmid:33469842
[1]
data:geo:GSE8597
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:GSE8597
gaps array · 1 item
[0]
method:not_determinable
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
2026-11-01T17:01:19Z
independence
single_reader
evidence_check object · 2 fields
method
reordered
availability
null
calls
5
usage object · 3 fields
prompt_tokens
2052
completion_tokens
1252
cached_tokens
256
stages array · 1 item
[0] object · 4 fields
id
extraction
state
complete
reader
MiniMax-M3.1-Flash
provider
minimax
gaps array · 3 items
[0]
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:33469842
type
paper
label
pmid:33469842
[1] object · 3 fields
id
source:pmid:33469842
type
manuscript
label
PMID 33469842 full text
[2] object · 3 fields
id
data:geo:GSE8597
type
dataset
label
GEO GSE8597
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:33469842
type
paper
label
pmid:33469842
[1] object · 3 fields
id
source:pmid:33469842
type
manuscript
label
PMID 33469842 full text
[2] object · 3 fields
id
data:geo:GSE8597
type
dataset
label
GEO GSE8597
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-33469842
type
extraction
used array · 1 item
[0]
source:pmid:33469842
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE8597
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE8597
agent
agent:corpus-assay-engine
agents array · 2 items
[0] object · 3 fields
id
agent:corpus-assay-engine
type
software
label
Corpus assay engine
[1] object · 3 fields
id
agent:minimax-reader
type
software
label
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:33469842
parent_hash
sha256:4b9ebd5336351de7ebe508a8889d5f3424b35df8df247da421fd4246117ba4e1
fork_of
null
gaps array · 7 items
[0]
asset:data:geo:GSE8597 licence not read
[1]
asset:data:geo:GSE8597 not downloaded
[2]
execution.not_run
[3]
method.reader_named_unmapped
[4]
review.human_critique
[5]
review.independent_reader
[6]
review.machine_critique
assays array · 4 items
[0] object · 11 fields
role
data_generation
definition_id
transfection
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 2 items
[0]
aling in cancer. We recently have shown that knockdown of nicotinic acetylcholine receptor subunit
[1]
largely downregulated by exposure to CHRNA5 siRNA in MCF7 cells while the response of primary
order_basis
paper_text_order:185
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
microarray
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.93
evidence array · 1 item
[0]
ETHODS: Meta-analyses of large breast cancer microarray cohorts were used to evaluate the associatio
order_basis
paper_text_order:513
id
assay:2
[2] object · 11 fields
role
data_generation
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 2 items
[0]
rognosis. The results were validated through RT-qPCR analyses of multiple E2 treated cell lines,
[1]
nosis. The results were validated through RT-qPCR analyses of multiple E2 treated cell lines,
order_basis
paper_text_order:709
id
assay:3
[3] object · 11 fields
role
data_generation
definition_id
cell_culture
definition_version
99e1195c7d6f
required_operations array · 0 items
support_state
partial
source_hashes object · 1 field
assay_lexicon
99e1195c7d6f
confidence
0.99
evidence array · 2 items
[0]
tiple E2 treated cell lines, CHRNA5 depleted MCF7 cells and across a breast cancer patient cDN
[1]
downregulated by exposure to CHRNA5 siRNA in MCF7 cells while the response of primary ESR1 tar
order_basis
paper_text_order:777
id
assay:4
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33469842", "kind": "science-record", "revision": 3, "content_hash": "sha256:10d363c0fa9f703546e1c495535401e3e2dfcff97c2b49ed876b84fc21730fda", "created_at": "2026-11-01T17:34:38Z", "updated_at": "2026-11-01T21:24:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "CHRNA5 belongs to the secondary estrogen signaling network exhibiting prognostic significance in breast cancer.", "doi": "10.1007/s13402-020-00581-x", "pmid": "33469842", "authors": ["Huma Shehwana", "Ayse G Keskus", "Sila E Ozdemir", "Azer A Acikgöz", "Rumeysa Biyik-Sit", "Ilgin Cagnan", "Damla Gunes", "Ermira Jahja", "Sahika Cingir-Koker", "Gizem Olmezer", "Ceren Sucularli", "Ozlen Konu"], "journal": "Cellular oncology (Dordrecht, Netherlands)", "year": 2021, "abstract": "PURPOSE: Cholinergic signals can be important modulators of cellular signaling in cancer. We recently have shown that knockdown of nicotinic acetylcholine receptor subunit alpha 5, CHRNA5, diminishes the proliferative potential of breast cancer cells. However, modulation of CHRNA5 expression in the context of estrogen signaling and its prognostic implications in breast cancer remained unexplored.\nMETHODS: Meta-analyses of large breast cancer microarray cohorts were used to evaluate the association of CHRNA5 expression with estrogen (E2) treatment, estrogen receptor (ER) status and patient prognosis. The results were validated through RT-qPCR analyses of multiple E2 treated cell lines, CHRNA5 depleted MCF7 cells and across a breast cancer patient cDNA panel. We also calculated a predicted secondary (PS) score representing direct/indirect induction of gene expression by E2 based on a public dataset (GSE8597). Co-expression analysis was performed using a weighted gene co-expression network analysis (WGCNA) pipeline. Multiple other publicly available datasets such as CCLE, COSMIC and TCGA were also analyzed.\nRESULTS: Herein we found that CHRNA5 expression was induced by E2 in a dose- and time-dependent manner in breast cancer cell lines. ER- breast tumors exhibited higher CHRNA5 expression levels than ER+ tumors. Independent meta-analysis for survival outcome revealed that higher CHRNA5 expression was associated with a worse prognosis in untreated breast cancer patients. Furthermore, CHRNA5 and its co-expressed gene network emerged as secondarily induced targets of E2 stimulation. These targets were largely downregulated by exposure to CHRNA5 siRNA in MCF7 cells while the response of primary ESR1 targets was dependent on the direction of the PS-score. Moreover, primary and secondary target genes were uncoupled and clustered distinctly based on multiple public datasets.\nCONCLUSION: Our findings strongly associate increased expression of CHRNA5 and its co-expression network with secondary E2 signaling and a worse prognosis in breast cancer.", "claims": [{"id": "claim-method", "statement": "Independent meta-analysis for survival outcome revealed that higher CHRNA5 expression was associated with a worse prognosis in untreated breast cancer patients. Co-expression analysis was performed using a weighted gene co-expression network analysis (WGCNA) pipeline.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33469842", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Independent meta-analysis for survival outcome revealed that higher CHRNA5 expression was associated with a worse prognosis in untreated breast cancer patients."}, {"asset": "source:pmid:33469842", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Co-expression analysis was performed using a weighted gene co-expression network analysis (WGCNA) pipeline."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We also calculated a predicted secondary (PS) score representing direct/indirect induction of gene expression by E2 based on a public dataset (GSE8597).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33469842", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "We also calculated a predicted secondary (PS) score representing direct/indirect induction of gene expression by E2 based on a public dataset (GSE8597)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:33469842"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE8597"], "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": {}, "inputs": ["data:geo:GSE8597"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33469842", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1007/s13402-020-00581-x", "sha256": "sha256:7282181eaa198528984bdf3a5315ccc8eb60d9fbd4af2250074df8902fb8b91a", "bytes": 2136, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1007/s13402-020-00581-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12980715", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE8597", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE8597", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE8597", "version": null, "note": "We also calculated a predicted secondary (PS) score representing direct/indirect induction of gene expression by E2 based on a public dataset (GSE8597).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We also calculated a predicted secondary (PS) score representing direct/indirect induction of gene expression by E2 based on a public dataset (GSE8597).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM213318", "GSM213319", "GSM213320", "GSM213321", "GSM213322", "GSM213323", "GSM213324", "GSM213325", "GSM213326", "GSM213327", "GSM213328", "GSM213329", "GSM213330", "GSM213331", "GSM213332", "GSM213333"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression analysis of hormone treated MCF7 breast cancer cells in the presence or absence of cycloheximide", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE8597 not downloaded", "asset:data:geo:GSE8597 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "Independent meta-analysis for survival outcome and weighted gene co-expression network analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "Independent meta-analysis for survival outcome revealed that higher CHRNA5 expression was associated with a worse prognosis in untreated breast cancer patients. Co-expression analysis was performed using a weighted gene co-expression network analysis (WGCNA) pipeline."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (Independent meta-analysis for survival outcome and weighted gene co-expression network analysis (WGCNA)), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"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": {"tier": "R1", "reachable": true, "accessions": ["GSE8597"], "resolved_accessions": ["GSE8597"], "statements": ["We also calculated a predicted secondary (PS) score representing direct/indirect induction of gene expression by E2 based on a public dataset (GSE8597)."], "basis": "The paper names GSE8597 in GSE8597 and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:33469842", "data:geo:GSE8597"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE8597"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:01:19Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 2052, "completion_tokens": 1252, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:33469842", "type": "paper", "label": "pmid:33469842"}, {"id": "source:pmid:33469842", "type": "manuscript", "label": "PMID 33469842 full text"}, {"id": "data:geo:GSE8597", "type": "dataset", "label": "GEO GSE8597"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33469842", "type": "paper", "label": "pmid:33469842"}, {"id": "source:pmid:33469842", "type": "manuscript", "label": "PMID 33469842 full text"}, {"id": "data:geo:GSE8597", "type": "dataset", "label": "GEO GSE8597"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33469842", "type": "extraction", "used": ["source:pmid:33469842"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE8597", "type": "accession_resolution", "used": ["data:geo:GSE8597"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:33469842", "parent_hash": "sha256:4b9ebd5336351de7ebe508a8889d5f3424b35df8df247da421fd4246117ba4e1", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE8597 licence not read", "asset:data:geo:GSE8597 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["aling in cancer. We recently have shown that knockdown of nicotinic acetylcholine receptor subunit", "largely downregulated by exposure to CHRNA5 siRNA in MCF7 cells while the response of primary"], "order_basis": "paper_text_order:185", "id": "assay:1"}, {"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ETHODS: Meta-analyses of large breast cancer microarray cohorts were used to evaluate the associatio"], "order_basis": "paper_text_order:513", "id": "assay:2"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["rognosis. The results were validated through RT-qPCR analyses of multiple E2 treated cell lines,", "nosis. The results were validated through RT-qPCR analyses of multiple E2 treated cell lines,"], "order_basis": "paper_text_order:709", "id": "assay:3"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["tiple E2 treated cell lines, CHRNA5 depleted MCF7 cells and across a breast cancer patient cDN", "downregulated by exposure to CHRNA5 siRNA in MCF7 cells while the response of primary ESR1 tar"], "order_basis": "paper_text_order:777", "id": "assay:4"}]}