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

pmid:30728047

Focal adhesion kinase (FAK) activation by estrogens involves GPER in triple-negative breast cancer cells.

Damiano Cosimo Rigiracciolo · Maria Francesca Santolla · Rosamaria Lappano · Adele Vivacqua · Francesca Cirillo · Giulia Raffaella Galli · Marianna Talia · Lucia Muglia · Michele Pellegrino · Nijiro Nohata · Maria Teresa Di Martino · Marcello Maggiolini

Journal of experimental & clinical cancer research : CR · 2019 doi:10.1186/s13046-019-1056-8

Paper

complete

Experiment

complete

Data

partial

Analysis

complete

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:30728047
kind
science-record
content_hash
sha256:d6e3a438877488ad4ea73b677dd757fa30b7166d5f44dc63c57e8913c9b82856
schema
https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json
created_at
2026-11-01T15:40:42Z
updated_at
2026-11-01T22:43:47Z
generator object · 2 fields
name
corpus-assay-engine
run_id
reading-sci-2026-11-01
paper object · 10 fields
state
complete
title
Focal adhesion kinase (FAK) activation by estrogens involves GPER in triple-negative breast cancer cells.
doi
10.1186/s13046-019-1056-8
pmid
30728047
authors array · 12 items
[0]
Damiano Cosimo Rigiracciolo
[1]
Maria Francesca Santolla
[2]
Rosamaria Lappano
[3]
Adele Vivacqua
[4]
Francesca Cirillo
[5]
Giulia Raffaella Galli
[6]
Marianna Talia
[7]
Lucia Muglia
[8]
Michele Pellegrino
[9]
Nijiro Nohata
[10]
Maria Teresa Di Martino
[11]
Marcello Maggiolini
journal
Journal of experimental & clinical cancer research : CR
year
2019
abstract
BACKGROUND: Focal adhesion kinase (FAK) is a cytoplasmatic protein tyrosine kinase that associates with both integrins and growth factor receptors toward the adhesion, migration and invasion of cancer cells. The G-protein coupled estrogen receptor (GPER) has been involved in the stimulatory action of estrogens in breast tumor. In this study, we have investigated the engagement of FAK by GPER signaling in triple negative breast cancer (TNBC) cells. METHODS: Publicly available large-scale database and patient data sets derived from "The Cancer Genome Atlas" (TCGA; www.cbioportal.org ) were used to assess FAK expression in TNBC, non-TNBC tumors and normal breast tissues. MDA-MB 231 and SUM159 TNBC cells were used as model system. The levels of phosphorylated FAK, other transduction mediators and target genes were detected by western blotting analysis. Focal adhesion assay was carried out in order to determine the focal adhesion points and the formation of focal adhesions (FAs). Luciferase assays were performed to evaluate the promoters activity of c-FOS, EGR1 and CTGF upon GPER activation. The mRNA expression of the aforementioned genes was measured by real time-PCR. Boyden chamber and wound healing assays were used in order to evaluate cell migration. The statistical analysis was performed by ANOVA. RESULTS: We first determined by bioinformatic analysis that the mRNA expression levels of the gene encoding FAK, namely PTK2, is higher in TNBC respect to non-TNBC and normal breast tissues. Next, we found that estrogenic GPER signaling triggers Y397 FAK phosphorylation as well as the increase of focal adhesion points (FAs) in TNBC cells. Besides, we ascertained that GPER and FAK activation are involved in the STAT3 nuclear accumulation and gene expression changes. As biological counterpart, we show that FAK inhibition prevents the migration of TNBC cells upon GPER activation. CONCLUSIONS: The present data provide novel insights regarding the action of FAK in TNBC. Moreover, on the basis of our findings estrogenic GPER signaling may be considered among the transduction mechanisms engaging FAK toward breast cancer progression.
claims array · 2 items
[0] object · 6 fields
id
claim-method
statement
The statistical analysis was performed using ANOVA followed by Newman–Keuls’ testing to determine differences in means.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:30728047
locator
sections[13] "Statistical analysis" paragraph 2
quote
The statistical analysis was performed using ANOVA followed by Newman–Keuls’ testing to determine differences in means.
state
complete
[1] object · 6 fields
id
claim-data-access
statement
Availability of data and materialsNot applicable.
kind
methodological
target
null
evidence array · 1 item
[0] object · 3 fields
asset
source:pmid:30728047
locator
sections[24] "ack" paragraph 1
quote
Availability of data and materialsNot applicable.
state
complete
gaps array · 0 items
experiment object · 8 fields
state
complete
objective
null
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:30728047
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:GSE38959
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:GSE38959
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:30728047
role
manuscript
format
xml
media_type
application/xml
uri
https://doi.org/10.1186/s13046-019-1056-8
sha256
sha256:94539b9973ac4ac9f284d5873edb77cdc2f79f3ccbad18c6cf6390febc2ad3ca
bytes
45770
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
10.1186/s13046-019-1056-8
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
PMC6364402
source
europe_pmc_fulltext
coverage
whole_body_without_references
text_hash_scope
rendered_section_body
[1] object · 15 fields
id
data:geo:GSE38959
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=GSE38959
sha256
null
bytes
null
access
open
state
resolved
reader
null
reader_status
reader_required
identifier
GSE38959
version
null
note
Availability of data and materialsNot applicable.
structure object · 15 fields
repository
GEO
access_route
GEO accession URL
access_statement_verbatim
Availability of data and materialsNot applicable.
access_statement_kind
data_availability_statement
sample_accessions array · 47 items
[0]
GSM952871
[1]
GSM952872
[2]
GSM952873
[3]
GSM952874
[4]
GSM952875
[5]
GSM952876
[6]
GSM952877
[7]
GSM952878
[8]
GSM952879
[9]
GSM952880
[10]
GSM952881
[11]
GSM952882
[12]
GSM952883
[13]
GSM952884
[14]
GSM952885
[15]
GSM952886
[16]
GSM952887
[17]
GSM952888
[18]
GSM952889
[19]
GSM952890
[20]
GSM952891
[21]
GSM952892
[22]
GSM952893
[23]
GSM952894
[24]
GSM952895
[25]
GSM952896
[26]
GSM952897
[27]
GSM952898
[28]
GSM952899
[29]
GSM952900
[30]
GSM952901
[31]
GSM952902
[32]
GSM952903
[33]
GSM952904
[34]
GSM952905
[35]
GSM952906
[36]
GSM952907
[37]
GSM952908
[38]
GSM952909
[39]
GSM952910
[40]
GSM952911
[41]
GSM952912
[42]
GSM952913
[43]
GSM952914
[44]
GSM952915
[45]
GSM952916
[46]
GSM952917
sample_count
47
group_sizes
null
group_sizes_basis
null
platform
4133
taxon
Homo sapiens
title
Gene expression profiling of triple negative breast cancer, normal ductal cells, and normal tissues
resolution_checked_at
2026-11-01T15:39:54Z
resolution_check
identifier_resolution_only_no_download_no_licence_read
downloaded
false
licence_read
false
gaps array · 2 items
[0]
asset:data:geo:GSE38959 not downloaded
[1]
asset:data:geo:GSE38959 licence not read
analysis object · 4 fields
state
complete
methods array · 3 items
[0] object · 10 fields
id
method-1
family
group_comparison
specific
anova
label
Group comparison
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
two_or_more_groups_continuous
evidence object · 3 fields
score
1
band
verbatim
quote
The statistical analysis was performed using ANOVA followed by Newman–Keuls’ testing to determine differences in means.
[1] object · 10 fields
id
method-2
family
survival_analysis
specific
kaplan_meier
label
Survival analysis
dsl_operations array · 1 item
[0]
survival_km
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
0.8
band
high
quote
Kaplan-Meier
[2] object · 10 fields
id
method-3
family
survival_analysis
specific
log_rank_test
label
Survival analysis
dsl_operations array · 1 item
[0]
logrank_test
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[0]
time_to_event_with_censoring
evidence object · 3 fields
score
0.8
band
high
quote
log-rank
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 · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
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: anova.
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]
GSE38959
resolved_accessions array · 1 item
[0]
GSE38959
statements array · 1 item
[0]
Availability of data and materialsNot applicable.
basis
The paper names GSE38959 in NCBI Gene Expression Omnibus (GEO) archive and the accession resolves in the repository. No dataset was downloaded and no licence was read.
can_run object · 3 fields
dsl_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
assets array · 2 items
[0]
source:pmid:30728047
[1]
data:geo:GSE38959
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:GSE38959
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
2026-10-31T18:13:49Z
independence
single_reader
evidence_check object · 2 fields
method
verbatim
availability
verbatim
calls
3
usage object · 3 fields
prompt_tokens
35275
completion_tokens
1726
cached_tokens
784
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:30728047
type
paper
label
pmid:30728047
[1] object · 3 fields
id
source:pmid:30728047
type
manuscript
label
PMID 30728047 full text
[2] object · 3 fields
id
data:geo:GSE38959
type
dataset
label
GEO GSE38959
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:30728047
type
paper
label
pmid:30728047
[1] object · 3 fields
id
source:pmid:30728047
type
manuscript
label
PMID 30728047 full text
[2] object · 3 fields
id
data:geo:GSE38959
type
dataset
label
GEO GSE38959
agent
agent:corpus-assay-engine
[1] object · 4 fields
id
activity-read-30728047
type
extraction
used array · 1 item
[0]
source:pmid:30728047
agent
agent:minimax-reader
[2] object · 4 fields
id
activity-resolve-GSE38959
type
accession_resolution
used array · 1 item
[0]
data:geo:GSE38959
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:30728047
parent_hash
sha256:d4ba6219f1242f1a02b16448a80788df002db860de064c18c909acf749d470a2
fork_of
null
gaps array · 6 items
[0]
asset:data:geo:GSE38959 licence not read
[1]
asset:data:geo:GSE38959 not downloaded
[2]
execution.not_run
[3]
review.human_critique
[4]
review.independent_reader
[5]
review.machine_critique
assays array · 3 items
[0] object · 11 fields
role
data_generation
definition_id
western_blot
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]
mediators and target genes were detected by western blotting analysis. Focal adhesion assay was carried o
[1]
bator with 5% CO2. Cells to be processed for immunoblot and RT-PCR assays were switched to medium wi
order_basis
paper_text_order:896
id
assay:1
[1] object · 11 fields
role
data_generation
definition_id
rna_seq
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]
(http://cbioportal.org). The analysis of the RNA sequencing data derived from Invasive Breast Cancer Coh
order_basis
paper_text_order:3765
id
assay:2
[2] object · 11 fields
role
analysis
definition_id
group_comparison
definition_version
f2132e96ae6c7a4e
required_operations array · 4 items
[0]
group_summary
[1]
welch_t
[2]
bootstrap_mean_difference
[3]
group_comparison_anova
support_state
supported
source_hashes object · 1 field
dsl_catalogue
f2132e96ae6c7a4e
evidence array · 1 item
[0]
The statistical analysis was performed using ANOVA followed by Newman–Keuls’ testing to determine differences in means.
order_basis
consumes_earlier_output
id
assay:3
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30728047", "kind": "science-record", "revision": 8, "content_hash": "sha256:d6e3a438877488ad4ea73b677dd757fa30b7166d5f44dc63c57e8913c9b82856", "created_at": "2026-11-01T15:40:42Z", "updated_at": "2026-11-01T22:43:47Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Focal adhesion kinase (FAK) activation by estrogens involves GPER in triple-negative breast cancer cells.", "doi": "10.1186/s13046-019-1056-8", "pmid": "30728047", "authors": ["Damiano Cosimo Rigiracciolo", "Maria Francesca Santolla", "Rosamaria Lappano", "Adele Vivacqua", "Francesca Cirillo", "Giulia Raffaella Galli", "Marianna Talia", "Lucia Muglia", "Michele Pellegrino", "Nijiro Nohata", "Maria Teresa Di Martino", "Marcello Maggiolini"], "journal": "Journal of experimental & clinical cancer research : CR", "year": 2019, "abstract": "BACKGROUND: Focal adhesion kinase (FAK) is a cytoplasmatic protein tyrosine kinase that associates with both integrins and growth factor receptors toward the adhesion, migration and invasion of cancer cells. The G-protein coupled estrogen receptor (GPER) has been involved in the stimulatory action of estrogens in breast tumor. In this study, we have investigated the engagement of FAK by GPER signaling in triple negative breast cancer (TNBC) cells.\nMETHODS: Publicly available large-scale database and patient data sets derived from \"The Cancer Genome Atlas\" (TCGA; www.cbioportal.org ) were used to assess FAK expression in TNBC, non-TNBC tumors and normal breast tissues. MDA-MB 231 and SUM159 TNBC cells were used as model system. The levels of phosphorylated FAK, other transduction mediators and target genes were detected by western blotting analysis. Focal adhesion assay was carried out in order to determine the focal adhesion points and the formation of focal adhesions (FAs). Luciferase assays were performed to evaluate the promoters activity of c-FOS, EGR1 and CTGF upon GPER activation. The mRNA expression of the aforementioned genes was measured by real time-PCR. Boyden chamber and wound healing assays were used in order to evaluate cell migration. The statistical analysis was performed by ANOVA.\nRESULTS: We first determined by bioinformatic analysis that the mRNA expression levels of the gene encoding FAK, namely PTK2, is higher in TNBC respect to non-TNBC and normal breast tissues. Next, we found that estrogenic GPER signaling triggers Y397 FAK phosphorylation as well as the increase of focal adhesion points (FAs) in TNBC cells. Besides, we ascertained that GPER and FAK activation are involved in the STAT3 nuclear accumulation and gene expression changes. As biological counterpart, we show that FAK inhibition prevents the migration of TNBC cells upon GPER activation.\nCONCLUSIONS: The present data provide novel insights regarding the action of FAK in TNBC. Moreover, on the basis of our findings estrogenic GPER signaling may be considered among the transduction mechanisms engaging FAK toward breast cancer progression.", "claims": [{"id": "claim-method", "statement": "The statistical analysis was performed using ANOVA followed by Newman–Keuls’ testing to determine differences in means.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30728047", "locator": "sections[13] \"Statistical analysis\" paragraph 2", "quote": "The statistical analysis was performed using ANOVA followed by Newman–Keuls’ testing to determine differences in means."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Availability of data and materialsNot applicable.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30728047", "locator": "sections[24] \"ack\" paragraph 1", "quote": "Availability of data and materialsNot applicable."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:30728047"], "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:GSE38959"], "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:GSE38959"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30728047", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13046-019-1056-8", "sha256": "sha256:94539b9973ac4ac9f284d5873edb77cdc2f79f3ccbad18c6cf6390febc2ad3ca", "bytes": 45770, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s13046-019-1056-8", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6364402", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE38959", "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=GSE38959", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE38959", "version": null, "note": "Availability of data and materialsNot applicable.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Availability of data and materialsNot applicable.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM952871", "GSM952872", "GSM952873", "GSM952874", "GSM952875", "GSM952876", "GSM952877", "GSM952878", "GSM952879", "GSM952880", "GSM952881", "GSM952882", "GSM952883", "GSM952884", "GSM952885", "GSM952886", "GSM952887", "GSM952888", "GSM952889", "GSM952890", "GSM952891", "GSM952892", "GSM952893", "GSM952894", "GSM952895", "GSM952896", "GSM952897", "GSM952898", "GSM952899", "GSM952900", "GSM952901", "GSM952902", "GSM952903", "GSM952904", "GSM952905", "GSM952906", "GSM952907", "GSM952908", "GSM952909", "GSM952910", "GSM952911", "GSM952912", "GSM952913", "GSM952914", "GSM952915", "GSM952916", "GSM952917"], "sample_count": 47, "group_sizes": null, "group_sizes_basis": null, "platform": "4133", "taxon": "Homo sapiens", "title": "Gene expression profiling of triple negative breast cancer, normal ductal cells, and normal tissues", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE38959 not downloaded", "asset:data:geo:GSE38959 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The statistical analysis was performed using ANOVA followed by Newman–Keuls’ testing to determine differences in means."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}], "targets": [], "gaps": []}, "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: anova."}, "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": ["GSE38959"], "resolved_accessions": ["GSE38959"], "statements": ["Availability of data and materialsNot applicable."], "basis": "The paper names GSE38959 in NCBI Gene Expression Omnibus (GEO) archive and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:30728047", "data:geo:GSE38959"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE38959"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:13:49Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 35275, "completion_tokens": 1726, "cached_tokens": 784}}, "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:30728047", "type": "paper", "label": "pmid:30728047"}, {"id": "source:pmid:30728047", "type": "manuscript", "label": "PMID 30728047 full text"}, {"id": "data:geo:GSE38959", "type": "dataset", "label": "GEO GSE38959"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30728047", "type": "paper", "label": "pmid:30728047"}, {"id": "source:pmid:30728047", "type": "manuscript", "label": "PMID 30728047 full text"}, {"id": "data:geo:GSE38959", "type": "dataset", "label": "GEO GSE38959"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30728047", "type": "extraction", "used": ["source:pmid:30728047"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE38959", "type": "accession_resolution", "used": ["data:geo:GSE38959"], "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:30728047", "parent_hash": "sha256:d4ba6219f1242f1a02b16448a80788df002db860de064c18c909acf749d470a2", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE38959 licence not read", "asset:data:geo:GSE38959 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["mediators and target genes were detected by western blotting analysis. Focal adhesion assay was carried o", "bator with 5% CO2. Cells to be processed for immunoblot and RT-PCR assays were switched to medium wi"], "order_basis": "paper_text_order:896", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["(http://cbioportal.org). The analysis of the RNA sequencing data derived from Invasive Breast Cancer Coh"], "order_basis": "paper_text_order:3765", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The statistical analysis was performed using ANOVA followed by Newman–Keuls’ testing to determine differences in means."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}