Identification of novel key genes associated with uterine corpus endometrial carcinoma progression and prognosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36819577", "kind": "science-record", "revision": 3, "content_hash": "sha256:1ee4977beb59658adc111c1136440465e1f3e4d434b3b44eec9b43a588ca60b1", "created_at": "2026-11-01T19:01:25Z", "updated_at": "2026-11-01T22:08:52Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of novel key genes associated with uterine corpus endometrial carcinoma progression and prognosis.", "doi": "10.21037/atm-22-6461", "pmid": "36819577", "authors": ["Haixia Li", "Quan Zhou", "Zhangying Wu", "Xiaoling Lu"], "journal": "Annals of translational medicine", "year": 2023, "abstract": "Background: Uterine corpus endometrial carcinoma (UCEC) is a common malignant cancer type which affects the health of women worldwide. However, its molecular mechanism has not been elucidated.\nMethods: To identify the hub modules and genes in UCEC associated with clinical phenotypes, the RNA sequencing data and clinical data of 543 UCEC samples were obtained from The Cancer Genome Atlas (TCGA) database and then subjected to weighted gene co-expression network analysis (WGCNA). To explore the potential biological function of the hub modules, Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted. Genes differentially expressed in UCEC were screened according to TCGA data using the \"gdcDEAnalysis\" package in R (The R Foundation for Statistical Computing). After intersecting with hub genes, the shared genes were used for further survival analyses. The relationship between gene expression level and clinical phenotype was analyzed in the TCGA-UCEC cohort in The University of ALabama at Birmingham CANcer data analysis Portal and the Human Protein Atlas. The microarray data set GSE17025 was also analyzed to validate the gene expression profiles.\nResults: There were 19 coexpression modules generated by WGCNA. Among them, 2 modules with 198 hub genes were highly correlated with clinical features (especially histologic grade and clinical stage). Meanwhile, 4,003 differentially expressed genes (DEGs) were screened out, and 164 DEGs overlapped with hub genes. Survival analyses revealed that high expression of GINS4 and low expression of ESR1 showed a trend of poor prognosis. Further analyses demonstrated that both messenger RNA (mRNA) and protein expression profiles of GINS4 and ESR1 were significantly associated with UCEC development and progression in TCGA and GSE17025 cohorts.\nConclusions: Based on the integrated bioinformatic analyses, our data indicated that GINS4 and ESR1 might serve as potential prognostic markers and targets for UCEC therapy.", "claims": [{"id": "claim-method", "statement": "WGCNA has been widely used to identify gene modules and genes of interest.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36819577", "locator": "sections[6] \"Construction of a weighted coexpression network\" paragraph 2", "quote": "WGCNA has been widely used to identify gene modules and genes of interest."}], "state": "complete"}, {"id": "claim-data-access", "statement": "RNA high-throughput sequencing counts and clinical information for patients with UCEC were directly downloaded from TCGA data repository (https://portal.gdc.cancer.gov/; Project ID: TCGA-UCEC).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36819577", "locator": "sections[4] \"Data collection and preparation\" paragraph 2", "quote": "RNA high-throughput sequencing counts and clinical information for patients with UCEC were directly downloaded from TCGA data repository (https://portal.gdc.cancer.gov/; Project ID: TCGA-UCEC)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Survival analyses revealed that high expression of GINS4 and low expression of ESR1 showed a trend of poor prognosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36819577", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Survival analyses revealed that high expression of GINS4 and low expression of ESR1 showed a trend of poor prognosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Survival analyses revealed that high expression of GINS4 and low expression of ESR1 showed a trend of poor prognosis.", "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:36819577"], "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:GSE17025"], "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:GSE17025"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36819577", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/atm-22-6461", "sha256": "sha256:51206573c61417fb96992d85ef843c82b3e7c2913c70713b7418531a6fa284c6", "bytes": 45982, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/atm-22-6461", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9929804", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE17025", "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=GSE17025", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17025", "version": null, "note": "RNA high-throughput sequencing counts and clinical information for patients with UCEC were directly downloaded from TCGA data repository (https://portal.gdc.cancer.gov/; Project ID: TCGA-UCEC).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "RNA high-throughput sequencing counts and clinical information for patients with UCEC were directly downloaded from TCGA data repository (https://portal.gdc.cancer.gov/; Project ID: TCGA-UCEC).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM425837", "GSM425838", "GSM425839", "GSM425840", "GSM425841", "GSM425842", "GSM425843", "GSM425844", "GSM425845", "GSM425846", "GSM425847", "GSM425848", "GSM425849", "GSM425850", "GSM425851", "GSM425852", "GSM425853", "GSM425854", "GSM425855", "GSM425856", "GSM425857", "GSM425858", "GSM425859", "GSM425860", "GSM425861", "GSM425862", "GSM425863", "GSM425864", "GSM425865", "GSM425866", "GSM425867", "GSM425868", "GSM425869", "GSM425870", "GSM425871", "GSM425872", "GSM425873", "GSM425874", "GSM425875", "GSM425876", "GSM425877", "GSM425878", "GSM425879", "GSM425880", "GSM425881", "GSM425882", "GSM425883", "GSM425884", "GSM425885", "GSM425886", "GSM425887", "GSM425888", "GSM425889", "GSM425890", "GSM425891", "GSM425892", "GSM425893", "GSM425894", "GSM425895", "GSM425896", "GSM425897", "GSM425898", "GSM425899", "GSM425900", "GSM425901", "GSM425902", "GSM425903", "GSM425904", "GSM425905", "GSM425906", "GSM425907", "GSM425908", "GSM425909", "GSM425910", "GSM425911", "GSM425912", "GSM425913", "GSM425914", "GSM425915", "GSM425916", "GSM425917", "GSM425918", "GSM425919", "GSM425920", "GSM425921", "GSM425922", "GSM425923", "GSM425924", "GSM425925", "GSM425926", "GSM425927", "GSM425928", "GSM425929", "GSM425930", "GSM425931", "GSM425932", "GSM425933", "GSM425934", "GSM425935", "GSM425936", "GSM425937", "GSM425938", "GSM425939"], "sample_count": 103, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene Expression Analysis of Stage I Endometrial Cancers", "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:GSE17025 not downloaded", "asset:data:geo:GSE17025 licence not read"]}, "analysis": {"state": "partial", "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": 0.8, "band": "high", "quote": "ANOVA"}}, {"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": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "Cox proportional hazards"}}, {"id": "method-4", "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": 0.8, "band": "high", "quote": "ROC analysis"}}, {"id": "method-5", "family": null, "specific": null, "label": "Weighted gene co-expression network analysis (WGCNA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "WGCNA has been widely used to identify gene modules and genes of interest."}}], "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": "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": ["GSE17025"], "resolved_accessions": ["GSE17025"], "statements": ["RNA high-throughput sequencing counts and clinical information for patients with UCEC were directly downloaded from TCGA data repository (https://portal.gdc.cancer.gov/; Project ID: TCGA-UCEC)."], "basis": "The paper names GSE17025 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": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "assets": ["source:pmid:36819577", "data:geo:GSE17025"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE17025"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:28:32Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 11865, "completion_tokens": 1894, "cached_tokens": 264}}, "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:36819577", "type": "paper", "label": "pmid:36819577"}, {"id": "source:pmid:36819577", "type": "manuscript", "label": "PMID 36819577 full text"}, {"id": "data:geo:GSE17025", "type": "dataset", "label": "GEO GSE17025"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36819577", "type": "paper", "label": "pmid:36819577"}, {"id": "source:pmid:36819577", "type": "manuscript", "label": "PMID 36819577 full text"}, {"id": "data:geo:GSE17025", "type": "dataset", "label": "GEO GSE17025"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36819577", "type": "extraction", "used": ["source:pmid:36819577"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE17025", "type": "accession_resolution", "used": ["data:geo:GSE17025"], "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:36819577", "parent_hash": "sha256:6b682861b6e8e5c5d7a1b3e3127da90b685c2c9b19d6b5fa1ec545b58a08fcfe", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE17025 licence not read", "asset:data:geo:GSE17025 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["CEC associated with clinical phenotypes, the RNA sequencing data and clinical data of 543 UCEC samples w"], "order_basis": "paper_text_order:358", "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": ["ysis Portal and the Human Protein Atlas. The microarray data set GSE17025 was also analyzed to valid"], "order_basis": "paper_text_order:1198", "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": 0.8, "evidence": ["ANOVA"], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}