Identification and immune landscape analysis of fatty acid metabolism genes related subtypes of gastric cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37993654", "kind": "science-record", "revision": 3, "content_hash": "sha256:b5d39f129712c3d729fd3c5c7b6c2d5a39dbdf7f89b4385f430e6e31d98826a3", "created_at": "2026-11-01T19:02:55Z", "updated_at": "2026-11-01T22:10:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and immune landscape analysis of fatty acid metabolism genes related subtypes of gastric cancer.", "doi": "10.1038/s41598-023-47631-6", "pmid": "37993654", "authors": ["Rong Huang", "Tai-Liang Lu", "Rui Zhou"], "journal": "Scientific reports", "year": 2023, "abstract": "Fatty acid metabolism (FAM) is associated with prognosis and immune microenvironment remodeling in many tumors. It is currently unknown how FAM affects the immunological microenvironment and prognosis of Gastric cancer (GC). Therefore, the current work aims to categorize GC samples based on the expression status of genes involved in FAM and to identify populations that might benefit from immunotherapy. In total, 50 FAM genes associated with overall survival (OS) were determined through univariate Cox proportional hazard regression analysis by mining the public TCGA and GEO databases. The GSE84437 and TCGA-STAD cohort samples were divided into two clusters using the \"NMF\" R package. According to the survival curve, patients in Cluster-1 showed considerably longer OS than those in Cluster-2. Patients in Cluster-1 exhibited earlier T stages, more intestinal GCs, and were older. MSI molecular subtypes were mainly distributed in Cluster-1, while GS molecular subtypes were distributed primarily in Cluster-2. There were 227 upregulated and 22 down-regulated genes (logFC > 1 or logFC < - 1, FDR < 0.05) in Cluster-2 compared with Cluster-1. One hub module (edges = 64, nodes = 12) was identified with a module score of 11.636 through Cytoscape plug-in MCODE. KEGG and GO analysis showed that the hub genes were associated with the cell cycle and cell division. Different immune cell infiltrates profile, and immune pathway enrichment existed between the subtypes. In conclusion, the current findings showed that practically all immunological checkpoint and immunoregulatory genes were elevated in patients with Cluster-2 GC, indicating that FAM subtypes may be crucial in GC immunotherapy.", "claims": [{"id": "claim-method", "statement": "50 FAM genes related to OS were picked out by univariate Cox proportional hazard regression (Supplementary Table S2).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37993654", "locator": "sections[3] \"Identification of FAM genes associated with prognosis in GC\" paragraph 2", "quote": "50 FAM genes related to OS were picked out by univariate Cox proportional hazard regression (Supplementary Table S2)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets ANALYZED for this study can be found in The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov/) and Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84437).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37993654", "locator": "sections[20] \"Data availability\" paragraph 2", "quote": "The datasets ANALYZED for this study can be found in The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov/) and Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE84437)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Fifty FAM genes associated with overall survival were identified using univariate Cox proportional hazard regression analysis of public TCGA and GEO data.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37993654", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In total, 50 FAM genes associated with overall survival (OS) were determined through univariate Cox proportional hazard regression analysis by mining the public TCGA and GEO databases."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Fifty FAM genes associated with overall survival were identified using univariate Cox proportional hazard regression analysis of public TCGA and GEO data.", "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:37993654"], "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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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:37993654", "data:geo:GSE84437"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE84437"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:00:08Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12855, "completion_tokens": 2179, "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:37993654", "type": "paper", "label": "pmid:37993654"}, {"id": "source:pmid:37993654", "type": "manuscript", "label": "PMID 37993654 full text"}, {"id": "data:geo:GSE84437", "type": "dataset", "label": "GEO GSE84437"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37993654", "type": "paper", "label": "pmid:37993654"}, {"id": "source:pmid:37993654", "type": "manuscript", "label": "PMID 37993654 full text"}, {"id": "data:geo:GSE84437", "type": "dataset", "label": "GEO GSE84437"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37993654", "type": "extraction", "used": ["source:pmid:37993654"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE84437", "type": "accession_resolution", "used": ["data:geo:GSE84437"], "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:37993654", "parent_hash": "sha256:0ca6f3877c8b464ed3f20cd56d4e13dbd4fed81d4b65463ad5c372d5a884d318", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE84437 licence not read", "asset:data:geo:GSE84437 not downloaded", "execution.not_run", "method.reader_named_unmapped", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Student's T test"], "order_basis": "analysis_only", "id": "assay:1"}]}