Predicting Panel of Metabolism and Immune-Related Genes for the Prognosis of Human Ovarian Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34322485", "kind": "science-record", "revision": 8, "content_hash": "sha256:690075c4a7aaba5a4c900519ce0bf9abf648cc6f50e289a4ad0fee581e43b9dd", "created_at": "2026-11-01T15:41:45Z", "updated_at": "2026-11-01T22:47:12Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Predicting Panel of Metabolism and Immune-Related Genes for the Prognosis of Human Ovarian Cancer.", "doi": "10.3389/fcell.2021.690542", "pmid": "34322485", "authors": ["Lingyun Zhang", "Wenwen Sun", "Weimin Ren", "Jinguo Zhang", "Guoxiong Xu"], "journal": "Frontiers in cell and developmental biology", "year": 2021, "abstract": "OBJECTIVE: Ovarian cancer (OC) is a high deadly gynecologic cancer with a poor prognosis. The identification of genomic aberrations could predict the clinical prognosis of OC patients and may eventually develop new therapeutic strategies in the future. The purpose of this study is to create comprehensive co-expressed gene networks correlated with metabolism and the immune process of OC.\nMETHODS: The transcriptome profiles of TCGA OC datasets and GSE26193 datasets were analyzed. The mRNA expression level, hub genomic alteration, patient's survival status, and tumor cell immune microenvironment of metabolism-related genes were analyzed from TCGA, GTEX, Oncomine, Kaplan-Meier Plotter, cBioPortal, TIMER, ESTIMATE, and CIBERSORT databases. We further validated the mRNA and protein expression levels of these hub genes in OC cell lines and tissues using qRT-PCR and immunohistochemistry.\nRESULTS: The LASSO-Cox regression analyses unveiled seven differently expressed metabolism-related genes, including GFPT2, DGKD, ACACB, ACSM3, IDO1, TPMT, and PGP. The Cox regression risk model could be served as an independent marker to predict the overall clinical survival of OC patients. The expression of GFPT2, DGKD, ACACB, and ACSM3 were downregulated in OC tissues, while IDO1, TPMT, and PGP were upregulated in OC tissues than in control. Moreover, DGKD and IDO1 were significantly associated with the human immune system.\nCONCLUSION: The differently expressed metabolism-related genes were identified to be a risk model in the prediction of the prognosis of OC. The identified hub genes related to OC prognosis may play important roles in influencing both human metabolism and the immune system.", "claims": [{"id": "claim-method", "statement": "We screened 91 differently expressed metabolism-related genes by the “limma” R package in TCGA-OV dataset compare to GTEX normal tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34322485", "locator": "sections[4] \"Detection of Differently Metabolism-Related Genes\" paragraph 2", "quote": "We screened 91 differently expressed metabolism-related genes by the “limma” R package in TCGA-OV dataset compare to GTEX normal tissues."}], "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:34322485", "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"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:34322485"], "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:GSE26193"], "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:GSE26193"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34322485", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fcell.2021.690542", "sha256": "sha256:6d3f97f4da3db736661b519229d0a005e59d98e2f3eec8d8b5acf56198e9b2a8", "bytes": 57215, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fcell.2021.690542", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8312230", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE26193", "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=GSE26193", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26193", "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": ["GSM642933", "GSM642934", "GSM642935", "GSM642936", "GSM642937", "GSM642938", "GSM642939", "GSM642940", "GSM642941", "GSM642942", "GSM642943", "GSM642944", "GSM642945", "GSM642946", "GSM642947", "GSM642948", "GSM642949", "GSM642950", "GSM642951", "GSM642952", "GSM642953", "GSM642954", "GSM642955", "GSM642956", "GSM642957", "GSM642958", "GSM642959", "GSM642960", "GSM642961", "GSM642962", "GSM642963", "GSM642964", "GSM642965", "GSM642966", "GSM642967", "GSM642968", "GSM642969", "GSM642970", "GSM642971", "GSM642972", "GSM642973", "GSM642974", "GSM642975", "GSM642976", "GSM642977", "GSM642978", "GSM642979", "GSM642980", "GSM642981", "GSM642982", "GSM642983", "GSM642984", "GSM642985", "GSM642986", "GSM642987", "GSM642988", "GSM642989", "GSM642990", "GSM642991", "GSM642992", "GSM642993", "GSM642994", "GSM642995", "GSM642996", "GSM642997", "GSM642998", "GSM642999", "GSM643000", "GSM643001", "GSM643002", "GSM643003", "GSM643004", "GSM643005", "GSM643006", "GSM643007", "GSM643008", "GSM643009", "GSM643010", "GSM643011", "GSM643012", "GSM643013", "GSM643014", "GSM643015", "GSM643016", "GSM643017", "GSM643018", "GSM643019", "GSM643020", "GSM643021", "GSM643022", "GSM643023", "GSM643024", "GSM643025", "GSM643026", "GSM643027", "GSM643028", "GSM643029", "GSM643030", "GSM643031", "GSM643032", "GSM643033", "GSM643034", "GSM643035", "GSM643036", "GSM643037", "GSM643038", "GSM643039"], "sample_count": 107, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Control of oxidative stress by miRNA and impact on ovarian tumorigenesis", "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:GSE26193 not downloaded", "asset:data:geo:GSE26193 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "We screened 91 differently expressed metabolism-related genes by the “limma” R package in TCGA-OV dataset compare to GTEX normal tissues."}}, {"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": 0.7, "band": "medium", "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": 0.7, "band": "medium", "quote": "Cox regression"}}, {"id": "method-4", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {"hazard_ratio": "ence intervals (CIs) of hazard ratio (HR) and log-rank P-val", "p_value": "ratio (HR) and log-rank P-value were counted"}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.8, "band": "high", "quote": "log-rank"}}, {"id": "method-5", "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": 0.8, "band": "high", "quote": "PPI"}}, {"id": "method-6", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "Go enrichment"}}], "targets": [], "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE26193"], "resolved_accessions": ["GSE26193"], "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 GSE26193 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:34322485", "data:geo:GSE26193"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE26193"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:33:05Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 45681, "completion_tokens": 2306, "cached_tokens": 785}}, "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:34322485", "type": "paper", "label": "pmid:34322485"}, {"id": "source:pmid:34322485", "type": "manuscript", "label": "PMID 34322485 full text"}, {"id": "data:geo:GSE26193", "type": "dataset", "label": "GEO GSE26193"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34322485", "type": "paper", "label": "pmid:34322485"}, {"id": "source:pmid:34322485", "type": "manuscript", "label": "PMID 34322485 full text"}, {"id": "data:geo:GSE26193", "type": "dataset", "label": "GEO GSE26193"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34322485", "type": "extraction", "used": ["source:pmid:34322485"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE26193", "type": "accession_resolution", "used": ["data:geo:GSE26193"], "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:34322485", "parent_hash": "sha256:30dda69f06506cbe28cf25011258a04942b9143a71efd1a1e38e39ddfaa90466", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE26193 licence not read", "asset:data:geo:GSE26193 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": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["OC cell lines and tissues using qRT-PCR and immunohistochemistry. RESULTS: The LASSO-Cox regression analyses"], "order_basis": "paper_text_order:926", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["We screened 91 differently expressed metabolism-related genes by the “limma” R package in TCGA-OV dataset compare to GTEX normal tissues."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}