Identifying colorectal cancer subtypes and establishing a prognostic model using metabolic plasticity and ferroptosis genes.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39516556", "kind": "science-record", "revision": 3, "content_hash": "sha256:75ed1ae07fa94a181cfd00c88ab04b34138e1b12e22cc9ea26dfa949f7ec2279", "created_at": "2026-11-01T20:29:46Z", "updated_at": "2026-11-01T22:13:05Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identifying colorectal cancer subtypes and establishing a prognostic model using metabolic plasticity and ferroptosis genes.", "doi": "10.1038/s41598-024-78505-0", "pmid": "39516556", "authors": ["Jingwen Guan", "Simin Min", "Yan Xia", "Zhiguo Guo", "Xiaolan Zhou"], "journal": "Scientific reports", "year": 2024, "abstract": "Metabolic plasticity and ferroptosis are essential for colorectal cancer (CRC) progression. The effects and prognostic value of metabolic plasticity- and ferroptosis-related genes (MPFRGs) in CRC remain unclear. We established a prognostic model for CRC patients by identifying important genes in metabolic plasticity and ferroptosis. Data of CRC patients were retrieved from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus; MPFRG data were obtained from GeneCards and FerrDb. We performed functional (to explore differences between the two metabolic subtypes) and single-sample gene set (to assess the immune environment) enrichment analyses. Immunophenotype, tumor immunological dysfunction, and exclusion scores were assessed to determine patient immune responses. A least absolute shrinkage and selection operator-Cox regression model comprising 10 significant differentially expressed genes of metabolic plasticity and ferroptosis (MPFDEGs) was constructed using TCGA training cohort and validated using the GSE17536 and GSE39582 datasets. We established a nomogram comprising metabolic plasticity- and ferroptosis-based signatures, revealing the clinical application and potential molecular mechanisms underlying the role of MPFRGs in CRC. Our model (developed based on 10 MPFDEGs) is efficient for calculating the overall survival of CRC patients. Our findings provide new strategies for the clinical management and individualized treatment of these patients.", "claims": [{"id": "claim-method", "statement": "A least absolute shrinkage and selection operator-Cox regression model comprising 10 significant differentially expressed genes of metabolic plasticity and ferroptosis (MPFDEGs) was constructed using TCGA training cohort and validated using the GSE17536 and GSE39582 datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39516556", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A least absolute shrinkage and selection operator-Cox regression model comprising 10 significant differentially expressed genes of metabolic plasticity and ferroptosis (MPFDEGs) was constructed using TCGA training cohort and validated using the GSE17536 and GSE39582 datasets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data are publicly accessible, open access, and can be accessed upon reasonable request. Data relevant to this study are included in the article or uploaded as supplemental information. The CRC series used in this study is available in TCGA (https://portal.gdc.cancer.gov/), which are public repositories for functional genomics data.Gene expression data from the GEO repository (https://www.ncbi.nlm.nih.gov/geo/) include the following datasets: GSE17536, GSE39582.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39516556", "locator": "sections[29] \"notes\" paragraph 1", "quote": "All data are publicly accessible, open access, and can be accessed upon reasonable request. Data relevant to this study are included in the article or uploaded as supplemental information. The CRC series used in this study is available in TCGA (https://portal.gdc.cancer.gov/), which are public repositories for functional genomics data.Gene expression data from the GEO repository (https://www.ncbi.nlm.nih.gov/geo/) include the following datasets: GSE17536, GSE39582."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A 10-MPFDEG least absolute shrinkage and selection operator-Cox model was constructed using the TCGA training cohort and validated in the GSE17536 and GSE39582 datasets to estimate overall survival in colorectal cancer patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39516556", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "A least absolute shrinkage and selection operator-Cox regression model comprising 10 significant differentially expressed genes of metabolic plasticity and ferroptosis (MPFDEGs) was constructed using TCGA training cohort and validated using the GSE17536 and GSE39582 datasets."}, {"asset": "source:pmid:39516556", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Our model (developed based on 10 MPFDEGs) is efficient for calculating the overall survival of CRC patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A 10-MPFDEG least absolute shrinkage and selection operator-Cox model was constructed using the TCGA training cohort and validated in the GSE17536 and GSE39582 datasets to estimate overall survival in colorectal cancer patients.", "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:39516556"], "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:GSE17536"], "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:GSE17536"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39516556", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-024-78505-0", "sha256": "sha256:d060f803b3921a5f3ecc6e72bf69fa68309a4689e8b8b6b17dfee830e3b705d2", "bytes": 46699, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-024-78505-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11549462", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE17536", "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=GSE17536", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17536", "version": null, "note": "All data are publicly accessible, open access, and can be accessed upon reasonable request. Data relevant to this study are included in the article or uploaded as supplemental information. The CRC series used in this study is available in TCGA (https://portal.gdc.cancer.gov/), which are public repositories for functional genomics data.Gene expression data from the GEO repository (https://www.ncbi.nlm.nih.gov/geo/) include the following datasets: GSE17536, GSE39582.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data are publicly accessible, open access, and can be accessed upon reasonable request. Data relevant to this study are included in the article or uploaded as supplemental information. The CRC series used in this study is available in TCGA (https://portal.gdc.cancer.gov/), which are public repositories for functional genomics data.Gene expression data from the GEO repository (https://www.ncbi.nlm.nih.gov/geo/) include the following datasets: GSE17536, GSE39582.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM437093", "GSM437094", "GSM437095", "GSM437096", "GSM437097", "GSM437098", "GSM437099", "GSM437100", "GSM437101", "GSM437102", "GSM437103", "GSM437104", "GSM437105", "GSM437106", "GSM437107", "GSM437108", "GSM437109", "GSM437110", "GSM437111", "GSM437112", "GSM437113", "GSM437114", "GSM437115", "GSM437116", "GSM437117", "GSM437118", "GSM437119", "GSM437120", "GSM437121", "GSM437122", "GSM437123", "GSM437124", "GSM437125", "GSM437126", "GSM437127", "GSM437128", "GSM437129", "GSM437130", "GSM437131", "GSM437132", "GSM437133", "GSM437134", "GSM437135", "GSM437136", "GSM437137", "GSM437138", "GSM437139", "GSM437140", "GSM437141", "GSM437142", "GSM437143", "GSM437144", "GSM437145", "GSM437146", "GSM437147", "GSM437148", "GSM437149", "GSM437150", "GSM437151", "GSM437152", "GSM437153", "GSM437154", "GSM437155", "GSM437156", "GSM437157", "GSM437158", "GSM437159", "GSM437160", "GSM437161", "GSM437162", "GSM437163", "GSM437164", "GSM437165", "GSM437166", "GSM437167", "GSM437168", "GSM437169", "GSM437170", "GSM437171", "GSM437172", "GSM437173", "GSM437174", "GSM437175", "GSM437176", "GSM437177", "GSM437178", "GSM437179", "GSM437180", "GSM437181", "GSM437182", "GSM437183", "GSM437184", "GSM437185", "GSM437186", "GSM437187", "GSM437188", "GSM437189", "GSM437190", "GSM437191", "GSM437192", "GSM437193", "GSM437194", "GSM437195", "GSM437196", "GSM437197", "GSM437198", "GSM437199", "GSM437200", "GSM437201", "GSM437202", "GSM437203", "GSM437204", "GSM437205", "GSM437206", "GSM437207", "GSM437208", "GSM437209", "GSM437210", "GSM437211", "GSM437212", "GSM437213", "GSM437214", "GSM437215", "GSM437216", "GSM437217", "GSM437218", "GSM437219", "GSM437220", "GSM437221", "GSM437222", "GSM437223", "GSM437224", "GSM437225", "GSM437226", "GSM437227", "GSM437228", "GSM437229", "GSM437230", "GSM437231", "GSM437232", "GSM437233", "GSM437234", "GSM437235", "GSM437236", "GSM437237", "GSM437238", "GSM437239", "GSM437240", "GSM437241", "GSM437242", "GSM437243", "GSM437244", "GSM437245", "GSM437246", "GSM437247", "GSM437248", "GSM437249", "GSM437250", "GSM437251", "GSM437252", "GSM437253", "GSM437254", "GSM437255", "GSM437256", "GSM437257", "GSM437258", "GSM437259", "GSM437260", "GSM437261", "GSM437262", "GSM437263", "GSM437264", "GSM437265", "GSM437266", "GSM437267", "GSM437268", "GSM437269"], "sample_count": 177, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Metastasis Gene Expression Profile Predicts Recurrence and Death in Colon Cancer Patients (Moffitt Samples)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE39582", "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=GSE39582", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE39582", "version": null, "note": "All data are publicly accessible, open access, and can be accessed upon reasonable request. Data relevant to this study are included in the article or uploaded as supplemental information. The CRC series used in this study is available in TCGA (https://portal.gdc.cancer.gov/), which are public repositories for functional genomics data.Gene expression data from the GEO repository (https://www.ncbi.nlm.nih.gov/geo/) include the following datasets: GSE17536, GSE39582.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data are publicly accessible, open access, and can be accessed upon reasonable request. Data relevant to this study are included in the article or uploaded as supplemental information. 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