An autophagy-related diagnostic biomarker for uterine fibroids: FOS.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37138755", "kind": "science-record", "revision": 4, "content_hash": "sha256:eea66ac2ec3dc1d13f86719ece337c025d82049f5f726853ae29ef8c34121de5", "created_at": "2026-11-01T19:01:48Z", "updated_at": "2026-11-01T22:51:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "An autophagy-related diagnostic biomarker for uterine fibroids: FOS.", "doi": "10.3389/fmed.2023.1153537", "pmid": "37138755", "authors": ["Lei Cai", "Jie Li", "Rui Long", "Zhiqi Liao", "Juejun Gong", "Bowen Zheng", "Hanwang Zhang"], "journal": "Frontiers in medicine", "year": 2023, "abstract": "Uterine fibroids (UFs) are the most common benign gynecologic tumors in reproductive-aged women. The typical diagnostic strategies of UFs are transvaginal ultrasonography and pathological feature, while molecular biomarkers are considered conventional options in the assessment of the origin and development of UFs in recent years. Here, we extracted the differential expression genes (DEGs) and differential DNA methylation genes (DMGs) of UFs from the Gene Expression Omnibus (GEO) database, GSE64763, GSE120854, GSE45188, and GSE45187. 167 DEGs with aberrant DNA methylation were identified, and further Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) were performed by the relevant R package. We next discerned 2 hub genes (FOS, and TNFSF10) with autophagy involvement by overlapping 167 DEGs and 232 autophagic regulators from Human Autophagy Database. FOS was identified as the most crucial gene through the Protein-Protein Interactions (PPI) network with the correlation of the immune scores. Moreover, the down-regulated expression of FOS in UFs tissue at both mRNA and protein levels was validated by RT-qPCR and immunohistochemistry respectively. The area under the ROC curve (AUC) of FOS was 0.856, with a sensitivity of 86.2% and a specificity of 73.9%. Overall, we explored the possible biomarker of UFs undergoing DNA-methylated autophagy and provided clinicians with a comprehensive assessment of UFs.", "claims": [{"id": "claim-method", "statement": "The “pROC” package (version 1.18.0) was used for ROC curve analysis and the area under the curve (AUC) was used to estimate the diagnostic value of key genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37138755", "locator": "sections[14] \"2.12. ROC curve analysis\" paragraph 2", "quote": "The “pROC” package (version 1.18.0) was used for ROC curve analysis and the area under the curve (AUC) was used to estimate the diagnostic value of key genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37138755", "locator": "sections[26] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The diagnosis model of FOS was built based on GSE64763. AUC was 0.856 (95% confidence interval: 75.2–95.9%), and the sensitivity and specificity were 0.862 and 0.739, respectively (Figure 6A).", "kind": "quantitative", "target": {"value": 0.856, "unit": "auc", "tolerance": null, "source": "The diagnosis model of FOS was built based on GSE64763. AUC was 0.856 (95% confidence interval: 75.2–95.9%), and the sensitivity and specificity were 0.862 and 0.739, respectively (Figure 6A)."}, "evidence": [{"asset": "source:pmid:37138755", "locator": "sections[23] \"3.7. Diagnostic value\" paragraph 2", "quote": "The diagnosis model of FOS was built based on GSE64763. AUC was 0.856 (95% confidence interval: 75.2–95.9%), and the sensitivity and specificity were 0.862 and 0.739, respectively (Figure 6A)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The diagnosis model of FOS was built based on GSE64763. AUC was 0.856 (95% confidence interval: 75.2–95.9%), and the sensitivity and specificity were 0.862 and 0.739, respectively (Figure 6A).", "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:37138755"], "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:GSE120854"], "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:GSE120854"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37138755", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fmed.2023.1153537", "sha256": "sha256:14c4592ef4f485f01017dbb67230a87bd36b86fb5e5c2524204f2aec4a1adef4", "bytes": 37721, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fmed.2023.1153537", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10150886", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE120854", "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=GSE120854", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE120854", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3417135", "GSM3417136", "GSM3417137", "GSM3417138", "GSM3417139", "GSM3417140", "GSM3417141", "GSM3417142", "GSM3417143", "GSM3417144", "GSM3417145", "GSM3417146", "GSM3417147", "GSM3417148", "GSM3417149", "GSM3417150", "GSM3417151", "GSM3417152", "GSM3417153", "GSM3417154", "GSM3417155", "GSM3417156", "GSM3417157", "GSM3417158", "GSM3417159", "GSM3417160", "GSM3417161", "GSM3417162", "GSM3417163", "GSM3417164", "GSM3417165", "GSM3417166", "GSM3417167", "GSM3417168"], "sample_count": 34, "group_sizes": null, "group_sizes_basis": null, "platform": "23976", "taxon": "Homo sapiens", "title": "Integrated epigenome, exome and transcriptome analyses reveal molecular subtypes and homeotic transformation in uterine fibroids [DNA methylation]", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE45187", "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=GSE45187", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45187", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1098769", "GSM1098770", "GSM1098771", "GSM1098772", "GSM1098773", "GSM1098774", "GSM1098775", "GSM1098776", "GSM1098777"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "13534", "taxon": "Homo sapiens", "title": "Epigenome analysis of uterin leiomyoma and myometrium with or without leiomyoma [Methylation data]", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE45188", "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=GSE45188", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE45188", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1098778", "GSM1098779", "GSM1098780", "GSM1098781", "GSM1098782", "GSM1098783", "GSM1098784", "GSM1098785", "GSM1098786"], "sample_count": 9, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Epigenome analysis of uterin leiomyoma and myometrium with or without leiomyoma [Expression data]", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE64763", "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=GSE64763", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE64763", "version": null, "note": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1579399", "GSM1579400", "GSM1579401", "GSM1579402", "GSM1579403", "GSM1579404", "GSM1579405", "GSM1579406", "GSM1579407", "GSM1579408", "GSM1579409", "GSM1579410", "GSM1579411", "GSM1579412", "GSM1579413", "GSM1579414", "GSM1579415", "GSM1579416", "GSM1579417", "GSM1579418", "GSM1579419", "GSM1579420", "GSM1579421", "GSM1579422", "GSM1579423", "GSM1579424", "GSM1579425", "GSM1579426", "GSM1579427", "GSM1579428", "GSM1579429", "GSM1579430", "GSM1579431", "GSM1579432", "GSM1579433", "GSM1579434", "GSM1579435", "GSM1579436", "GSM1579437", "GSM1579438", "GSM1579439", "GSM1579440", "GSM1579441", "GSM1579442", "GSM1579443", "GSM1579444", "GSM1579445", "GSM1579446", "GSM1579447", "GSM1579448", "GSM1579449", "GSM1579450", "GSM1579451", "GSM1579452", "GSM1579453", "GSM1579454", "GSM1579455", "GSM1579456", "GSM1579457", "GSM1579458", "GSM1579459", "GSM1579460", "GSM1579461", "GSM1579462", "GSM1579463", "GSM1579464", "GSM1579465", "GSM1579466", "GSM1579467", "GSM1579468", "GSM1579469", "GSM1579470", "GSM1579471", "GSM1579472", "GSM1579473", "GSM1579474", "GSM1579475", "GSM1579476", "GSM1579477"], "sample_count": 79, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Expression data from normal myometrium, leiomyomata, and leiomyosarcomas", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE120854 not downloaded", "asset:data:geo:GSE120854 licence not read", "asset:data:geo:GSE45187 not downloaded", "asset:data:geo:GSE45187 licence not read", "asset:data:geo:GSE45188 not downloaded", "asset:data:geo:GSE45188 licence not read", "asset:data:geo:GSE64763 not downloaded", "asset:data:geo:GSE64763 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "diagnostic_evaluation", "specific": "roc", "label": "Diagnostic test evaluation", "dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["reference_standard_and_test"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The “pROC” package (version 1.18.0) was used for ROC curve analysis and the area under the curve (AUC) was used to estimate the diagnostic value of key genes."}}, {"id": "method-2", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 0.8, "band": "high", "quote": "limma"}}, {"id": "method-3", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "PPI"}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": "build_graph", "expected_value": 0.856, "unit": "auc", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": ["method.reader_differs_from_extractor"]}, "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": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: roc."}, "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": ["GSE64763", "GSE120854", "GSE45187", "GSE45188"], "resolved_accessions": ["GSE64763", "GSE120854", "GSE45187", "GSE45188"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary material."], "basis": "The paper names GSE64763, GSE120854, GSE45187, GSE45188 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "assets": ["source:pmid:37138755", "data:geo:GSE120854"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE120854"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:38:20Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12395, "completion_tokens": 1477, "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:37138755", "type": "paper", "label": "pmid:37138755"}, {"id": "source:pmid:37138755", "type": "manuscript", "label": "PMID 37138755 full text"}, {"id": "data:geo:GSE120854", "type": "dataset", "label": "GEO GSE120854"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37138755", "type": "paper", "label": "pmid:37138755"}, {"id": "source:pmid:37138755", "type": "manuscript", "label": "PMID 37138755 full text"}, {"id": "data:geo:GSE120854", "type": "dataset", "label": "GEO GSE120854"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37138755", "type": "extraction", "used": ["source:pmid:37138755"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE120854", "type": "accession_resolution", "used": ["data:geo:GSE120854"], "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:37138755", "parent_hash": "sha256:7fe4e576aa6338bbbed77fdd8b945bfe390303a7aefb4b2a26529140747004c1", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE120854 licence not read", "asset:data:geo:GSE120854 not downloaded", "asset:data:geo:GSE45187 licence not read", "asset:data:geo:GSE45187 not downloaded", "asset:data:geo:GSE45188 licence not read", "asset:data:geo:GSE45188 not downloaded", "asset:data:geo:GSE64763 licence not read", "asset:data:geo:GSE64763 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["oth mRNA and protein levels was validated by RT-qPCR and immunohistochemistry respectively. The a", "mRNA and protein levels was validated by RT-qPCR and immunohistochemistry respectively. The a", "The expression of FOS was investigated using real-time quantitative PCR and IHC in the fibroid and paired myometrium"], "order_basis": "paper_text_order:1167", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["protein levels was validated by RT-qPCR and immunohistochemistry respectively. The area under the ROC curve (", "ive expression of FOS in the mRNA level. (B) Immunohistochemical results of typical samples from two groups,", "oups, all images were presented at 20-X. (C) IHC score. NM, normal myometrium, UFs, uterine f", "tigated using real-time quantitative PCR and IHC in the fibroid and paired myometrium from 20"], "order_basis": "paper_text_order:1180", "id": "assay:2"}, {"role": "analysis", "definition_id": "diagnostic_evaluation", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["confusion_counts", "roc_curve", "sensitivity_specificity", "solve_confusion_matrix", "classification_metrics", "published_precision_envelope"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The “pROC” package (version 1.18.0) was used for ROC curve analysis and the area under the curve (AUC) was used to estimate the diagnostic value of key genes."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}