← All .science files
pmid:37409787
Serum HSF1 is upregulated in endometriosis patients and serves as a potential diagnostic biomarker.
Hui-Ying Pan · Jing Wan
The Kaohsiung journal of medical sciences · 2023 doi:10.1002/kjm2.12723
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
paper object · 10 fields
authors array · 2 items
claims array · 3 items
[0] object · 6 fields
[1] object · 6 fields
evidence array · 1 item
[0] object · 3 fields
[2] object · 6 fields
target object · 4 fields
evidence array · 1 item
[0] object · 3 fields
gaps array · 0 items
experiment object · 8 fields
steps array · 3 items
[0] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[1] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
instruments array · 0 items
reagents array · 0 items
[2] object · 13 fields
parameters object · 0 fields
inputs array · 1 item
outputs array · 1 item
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
assets array · 2 items
[0] object · 15 fields
structure object · 4 fields
[1] object · 15 fields
structure object · 15 fields
sample_accessions array · 22 items
gaps array · 2 items
analysis object · 4 fields
methods array · 2 items
[0] object · 10 fields
dsl_operations array · 1 item
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 1 item
[1] object · 10 fields
dsl_operations array · 0 items
missing_operations array · 0 items
parameters object · 0 fields
data_shapes array · 0 items
targets array · 1 item
[0] object · 8 fields
gaps array · 1 item
capability object · 3 fields
requirements array · 1 item
[0] object · 6 fields
assay_families array · 9 items
gaps array · 0 items
readiness object · 8 fields
axes object · 3 fields
method object · 5 fields
required_operations array · 1 item
missing_operations array · 0 items
capability object · 4 fields
data object · 6 fields
accessions array · 1 item
resolved_accessions array · 1 item
statements array · 1 item
can_run object · 3 fields
dsl_operations array · 1 item
assets array · 2 items
steps array · 1 item
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
gaps array · 0 items
review object · 5 fields
machine_critique object · 5 fields
reader object · 5 fields
evidence_check object · 2 fields
usage object · 3 fields
stages array · 1 item
[0] object · 4 fields
gaps array · 3 items
provenance object · 7 fields
entities array · 3 items
activities array · 3 items
[0] object · 4 fields
used array · 3 items
[0] object · 3 fields
[1] object · 3 fields
[2] object · 3 fields
[1] object · 4 fields
agents array · 2 items
lineage object · 4 fields
gaps array · 7 items
assays array · 1 item
[0] object · 11 fields
required_operations array · 1 item
source_hashes object · 1 field
evidence array · 1 item
Complete file
{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37409787", "kind": "science-record", "revision": 2, "content_hash": "sha256:487bc44e881cca48d0dee48c88ff05cf01a268d829e64455ddf0f9d10feb8f26", "created_at": "2026-11-01T19:02:10Z", "updated_at": "2026-11-01T21:31:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Serum HSF1 is upregulated in endometriosis patients and serves as a potential diagnostic biomarker.", "doi": "10.1002/kjm2.12723", "pmid": "37409787", "authors": ["Hui-Ying Pan", "Jing Wan"], "journal": "The Kaohsiung journal of medical sciences", "year": 2023, "abstract": "Endometriosis (EMS) is a prevalent gynecological condition lacking reliable diagnostic biomarkers. This prospective study aimed to analyze the potential of serum heat shock transcription factor 1 (HSF1) as a diagnostic marker for EMS. Clinical features of 92 EMS patients and 52 controls were recorded, revealing significant differences in dysmenorrhea, dyspareunia, pelvic pain, nulliparity, and CA125 levels. Serum HSF1 was upregulated in EMS patients, with higher levels in American Society for Reproductive Medicine (ASRM) III/IV than ASRM I/II. Receiver operating characteristic curve analysis demonstrated good diagnostic function for serum HSF1 (AUC: 0.857, sensitivity: 91.30%, specificity: 63.46%). Serum HSF1, dysmenorrhea, dyspareunia, and nulliparity were independent risk factors for EMS, while dysmenorrhea and serum HSF1 were independent risk factors for EMS severity. Additionally, the GSE25628 dataset was downloaded from the GEO database for differential analysis of gene expression. The HSF1 downstream target genes PTGES3, HSP90AA1, and HSPB1 showed significant differential expression in EMS, suggesting their involvement in the regulatory mechanism of HSF1 in EMS.", "claims": [{"id": "claim-method", "statement": "Receiver operating characteristic (ROC) analysis was conducted to evaluate the diagnostic accuracy of serum HSF1 for EMS patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37409787", "locator": "sections[8] \"Statistical analysis\" paragraph 2", "quote": "Receiver operating characteristic (ROC) analysis was conducted to evaluate the diagnostic accuracy of serum HSF1 for EMS patients."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We downloaded the EMS dataset GSE25628, which includes eight cases of ectopic endometria from EMS patients and 6 cases of endometria from healthy women, from the Gene Expression Omnibus (GEO) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37409787", "locator": "sections[7] \"Bioinformatics\" paragraph 2", "quote": "We downloaded the EMS dataset GSE25628, which includes eight cases of ectopic endometria from EMS patients and 6 cases of endometria from healthy women, from the Gene Expression Omnibus (GEO) database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Based on ROC analysis, the cutoff value of serum HSF1 in EMS was 1.12 (area under the curve [AUC]: 0.857), with a sensitivity and specificity of 91.30% and 63.46%, respectively (p < 0.05, Figure 1C).", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Based on ROC analysis, the cutoff value of serum HSF1 in EMS was 1.12 (area under the curve [AUC]: 0.857), with a sensitivity and specificity of 91.30% and 63.46%, respectively (p < 0.05, Figure 1C)."}, "evidence": [{"asset": "source:pmid:37409787", "locator": "sections[11] \"Determination of serum HSF1 and its diagnostic value\" paragraph 2", "quote": "Based on ROC analysis, the cutoff value of serum HSF1 in EMS was 1.12 (area under the curve [AUC]: 0.857), with a sensitivity and specificity of 91.30% and 63.46%, respectively (p < 0.05, Figure 1C)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Based on ROC analysis, the cutoff value of serum HSF1 in EMS was 1.12 (area under the curve [AUC]: 0.857), with a sensitivity and specificity of 91.30% and 63.46%, respectively (p < 0.05, Figure 1C).", "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:37409787"], "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:GSE25628"], "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:GSE25628"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37409787", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1002/kjm2.12723", "sha256": "sha256:1fe37f24ba59fd194a8b0f0c28336f6d6d6fc48feca3a0fa6a5b0dcc265da794", "bytes": 28402, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1002/kjm2.12723", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11895919", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE25628", "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=GSE25628", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25628", "version": null, "note": "We downloaded the EMS dataset GSE25628, which includes eight cases of ectopic endometria from EMS patients and 6 cases of endometria from healthy women, from the Gene Expression Omnibus (GEO) database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded the EMS dataset GSE25628, which includes eight cases of ectopic endometria from EMS patients and 6 cases of endometria from healthy women, from the Gene Expression Omnibus (GEO) database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM629719", "GSM629720", "GSM629721", "GSM629722", "GSM629723", "GSM629724", "GSM629725", "GSM629726", "GSM629727", "GSM629728", "GSM629729", "GSM629730", "GSM629731", "GSM629732", "GSM629733", "GSM629734", "GSM629735", "GSM629736", "GSM629737", "GSM629738", "GSM629739", "GSM629740"], "sample_count": 22, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Endometriosis transcription profiling", "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:GSE25628 not downloaded", "asset:data:geo:GSE25628 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "regression_modelling", "specific": "logistic", "label": "Regression modelling", "dsl_operations": ["glm_logit_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["predictors_and_outcome"], "evidence": {"score": 0.8, "band": "high", "quote": "Logistic regression"}}, {"id": "method-2", "family": null, "specific": null, "label": "Receiver operating characteristic (ROC) analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Receiver operating characteristic (ROC) analysis was conducted to evaluate the diagnostic accuracy of serum HSF1 for EMS patients."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "glm_logit_fit", "expected_value": 0.05, "unit": "p-value", "tolerance": null, "state": "complete", "note": "The threshold the paper applied to its own result, as the paper states it. A run that reproduces the effect is judged against this threshold."}], "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": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["glm_logit_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: logistic."}, "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": ["GSE25628"], "resolved_accessions": ["GSE25628"], "statements": ["We downloaded the EMS dataset GSE25628, which includes eight cases of ectopic endometria from EMS patients and 6 cases of endometria from healthy women, from the Gene Expression Omnibus (GEO) database."], "basis": "The paper names GSE25628 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["glm_logit_fit"], "assets": ["source:pmid:37409787", "data:geo:GSE25628"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE25628"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:46:09Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 9106, "completion_tokens": 1458, "cached_tokens": 128}}, "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:37409787", "type": "paper", "label": "pmid:37409787"}, {"id": "source:pmid:37409787", "type": "manuscript", "label": "PMID 37409787 full text"}, {"id": "data:geo:GSE25628", "type": "dataset", "label": "GEO GSE25628"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37409787", "type": "paper", "label": "pmid:37409787"}, {"id": "source:pmid:37409787", "type": "manuscript", "label": "PMID 37409787 full text"}, {"id": "data:geo:GSE25628", "type": "dataset", "label": "GEO GSE25628"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37409787", "type": "extraction", "used": ["source:pmid:37409787"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE25628", "type": "accession_resolution", "used": ["data:geo:GSE25628"], "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:37409787", "parent_hash": "sha256:089b10f1a8e66965daee96baf9719597fdaa1d6ecf66490d3d316cc65b7b91a9", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE25628 licence not read", "asset:data:geo:GSE25628 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "regression_modelling", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["glm_logit_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Logistic regression"], "order_basis": "analysis_only", "id": "assay:1"}]}