Differential expression of immune related genes in high-grade ovarian serous carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31918995", "kind": "science-record", "revision": 3, "content_hash": "sha256:c7c231a850180dc119146e211b1bcbdda3721cde4e16ab8feb519bf958b5b28d", "created_at": "2026-11-01T17:33:18Z", "updated_at": "2026-11-01T21:22:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Differential expression of immune related genes in high-grade ovarian serous carcinoma.", "doi": "10.1016/j.ygyno.2019.12.019", "pmid": "31918995", "authors": ["Sharareh Siamakpour-Reihani", "Lauren Patterson Cobb", "Chen Jiang", "Dadong Zhang", "Rebecca A Previs", "Kouros Owzar", "Andrew B Nixon", "Angeles Alvarez Secord"], "journal": "Gynecologic oncology", "year": 2020, "abstract": "OBJECTIVE: To identify novel immunologic targets and biomarkers associated with overall survival (OS) in high-grade serous ovarian cancer (HGSC).\nMETHODS: In this retrospective study, microarray data from 51 HGSC specimens were analyzed (Affymetrix HG-U133A). A panel of 183 immune/inflammatory response related genes linked to 279 probe sets was constructed a priori and screened. Associations between gene expression and OS were assessed using logrank tests. Multiple testing was addressed within the False Discovery Rate (FDR) framework. For external validation, TCGA Ovarian dataset and five GSE publicly available HGSC datasets were evaluated.\nRESULTS: In Duke data, 110 probe sets linked to 83 immunologic/inflammatory-related genes were differentially expressed in tumors from long versus short-term HGSC survivors (adjusted p < 0.05). In TCGA, concordant with the results from the Duke discovery cohort, high expression of one probe (IL6R) demonstrated a consistent significance and concordant association with higher expression in long-term HGSC survivors (Duke q-value = 0.022) and improved OS in the TCGA dataset (p-value = 0.015, HR = 0.8). Thirteen genes in GSE14764 (N = 4) and GSE26712 (N = 9) datasets had significant p-values and consistent concordant with Duke Data. Despite the significant associations of gene expression and OS in the individual GSE datasets, in the GSE meta-analysis no genes were consistently concordant and significantly associated with survival.\nCONCLUSIONS: Evaluation of IL6R expression may be warranted based on higher expression in long-term survivors and association with improved survival in advanced HGSC. The other candidate genes may also be of worthy of further exploration to enhance immuno-oncology drug discovery.", "claims": [{"id": "claim-method", "statement": "Association between gene expression of each probe set and OS was assessed using a logrank test [25].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31918995", "locator": "sections[5] \"Statistical analysis and validation of the association between IT genes expression and overall survival (OS) in publically available TCGA and GSE databases\" paragraph 4", "quote": "Association between gene expression of each probe set and OS was assessed using a logrank test [25]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "For external confirmation, we used publicly available HGSC data from The Cancer Genome Atlas (TCGA-OV, N = 229)", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31918995", "locator": "sections[6] \"Confirmation cohorts\" paragraph 2", "quote": "For external confirmation, we used publicly available HGSC data from The Cancer Genome Atlas (TCGA-OV, N = 229)"}], "state": "complete"}, {"id": "claim-target-result", "statement": "In TCGA concordant with the results from the Duke discovery cohort, high expression of one probe (IL6R) demonstrated a consistent significance and concordant association with higher expression in long-term HGSC survivors (Duke q-value = 022) and improved OS in the TCGA dataset (p-value = 0.015, HR = 0.8).", "kind": "quantitative", "target": {"value": 0.8, "unit": "hazard ratio", "tolerance": null, "source": "In TCGA concordant with the results from the Duke discovery cohort, high expression of one probe (IL6R) demonstrated a consistent significance and concordant association with higher expression in long-term HGSC survivors (Duke q-value = 022) and improved OS in the TCGA dataset (p-value = 0.015, HR = 0.8)."}, "evidence": [{"asset": "source:pmid:31918995", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In TCGA concordant with the results from the Duke discovery cohort, high expression of one probe (IL6R) demonstrated a consistent significance and concordant association with higher expression in long-term HGSC survivors (Duke q-value = 022) and improved OS in the TCGA dataset (p-value = 0.015, HR = 0.8)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In TCGA concordant with the results from the Duke discovery cohort, high expression of one probe (IL6R) demonstrated a consistent significance and concordant association with higher expression in long-term HGSC survivors (Duke q-value = 022) and improved OS in the TCGA dataset (p-value = 0.015, HR = 0.8).", "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:31918995"], "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. 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A run that reproduces the effect is judged against this threshold."}], "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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE26712", "GSE18520", "GSE14764", "GSE19161"], "resolved_accessions": ["GSE26712", "GSE18520", "GSE14764", "GSE19161"], "statements": ["For external confirmation, we used publicly available HGSC data from The Cancer Genome Atlas (TCGA-OV, N = 229)"], "basis": "The paper names GSE26712, GSE18520, GSE14764, GSE19161 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": ["logrank_test"], "assets": ["source:pmid:31918995", "data:geo:GSE14764"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14764"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T16:59:09Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 7447, "completion_tokens": 2155, "cached_tokens": 0}}, "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:31918995", "type": "paper", "label": "pmid:31918995"}, {"id": "source:pmid:31918995", "type": "manuscript", "label": "PMID 31918995 full text"}, {"id": "data:geo:GSE14764", "type": "dataset", "label": "GEO GSE14764"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:31918995", "type": "paper", "label": "pmid:31918995"}, {"id": "source:pmid:31918995", "type": "manuscript", "label": "PMID 31918995 full text"}, {"id": "data:geo:GSE14764", "type": "dataset", "label": "GEO GSE14764"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-31918995", "type": "extraction", "used": ["source:pmid:31918995"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14764", "type": "accession_resolution", "used": ["data:geo:GSE14764"], "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:31918995", "parent_hash": "sha256:6d0927840d5e6566d355289474e3b59b9b66e8c2a40494783417add5b3efb25a", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE14764 licence not read", "asset:data:geo:GSE14764 not downloaded", "asset:data:geo:GSE18520 licence not read", "asset:data:geo:GSE18520 not downloaded", "asset:data:geo:GSE19161 licence not read", "asset:data:geo:GSE19161 not downloaded", "asset:data:geo:GSE26712 licence not read", "asset:data:geo:GSE26712 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["HGSC). METHODS: In this retrospective study, microarray data from 51 HGSC specimens were analyzed (A", "y data from 51 HGSC specimens were analyzed (Affymetrix HG-U133A). A panel of 183 immune/inflammator", "ll genes of interest were represented on the Affymetrix HG-U133A GeneChip. For example PD1 (also kno", "(also known as PDCD1) was represented on the Affymetrix HG-U133A GeneChip but the PD-L1 (also known"], "order_basis": "paper_text_order:227", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Association between gene expression of each probe set and OS was assessed using a logrank test [25]."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}