Integrated bioinformatics analysis of IFITM1 as a prognostic biomarker and investigation of its immunological role in prostate adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36591519", "kind": "science-record", "revision": 3, "content_hash": "sha256:54acd123762d14afd67e7f3d44fa4926d732d6dd1a3167cec9e7321809a6e085", "created_at": "2026-11-01T19:01:08Z", "updated_at": "2026-11-01T22:08:28Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated bioinformatics analysis of IFITM1 as a prognostic biomarker and investigation of its immunological role in prostate adenocarcinoma.", "doi": "10.3389/fonc.2022.1037535", "pmid": "36591519", "authors": ["Shaoyi Qiao", "Wuhe Zhang", "Yansheng Su", "Yao Jiang"], "journal": "Frontiers in oncology", "year": 2022, "abstract": "Introduction: Prostate adenocarcinoma (PRAD) is a highly aggressive malignancy with high mortality and poor prognosis, and its potential mechanism remains unclear. Our study aimed to identify novel markers for the prognosis of PRAD using bioinformatics technology.\nMethods: The GSE32571 dataset was downloaded from the GEO database, and analyzed via the limma R package to identify differentially expressed genes (DEGs) and differentially expressed immune score-related genes (DEISRGs). The immune-related genes (IRGs) were further obtained by overlapping DEISRGs and DEGs, and the core gene was identified via survival analysis. Furthermore, the expression level, prognostic value, and potential functions of the core gene were evaluated via multiple bioinformatics databases.\nResults: A total of 301 IRGs were identified from the GSE32571 dataset, and IFITM1 was a down-regulated gene in several types of cancer, including PRAD. Besides, low expression of IFITM1 was associated with a poor prognosis in PRAD. GSEA indicated that the vital pathways of IFITM1-associated genes were mainly enriched in primary immunodeficiency, Th17 cell differentiation, Th1, and Th2 cell differentiation, natural killer cell-mediated cytotoxicity, myeloid dendritic cell activation, regulation of leukocyte activation, etc. Furthermore, IFITM1 was closely correlated with 22 types of tumor-infiltrating immune cells.\nDiscussion: IFITM1 was a prognostic biomarker for PRAD patients, and it can be acted as a potential immune therapy target in PRAD.", "claims": [{"id": "claim-method", "statement": "The Kaplan–Meier method with the log-rank test was applied to compare the overall survival for different IFITM1 patterns.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36591519", "locator": "sections[9] \"Survival analysis for IFITM1\" paragraph 2", "quote": "The Kaplan–Meier method with the log-rank test was applied to compare the overall survival for different IFITM1 patterns."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36591519", "locator": "sections[28] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:36591519"], "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:GSE32448"], "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:GSE32448"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36591519", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2022.1037535", "sha256": "sha256:247be5b5b92ea31f107cb73cb508ce571668ba7377943de48989b3f6ff3608ba", "bytes": 39573, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2022.1037535", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9795034", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE32448", "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=GSE32448", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32448", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM802807", "GSM802808", "GSM802809", "GSM802810", "GSM802811", "GSM802812", "GSM802813", "GSM802814", "GSM802815", "GSM802816", "GSM802817", "GSM802818", "GSM802819", "GSM802820", "GSM802821", "GSM802822", "GSM802823", "GSM802824", "GSM802825", "GSM802826", "GSM802827", "GSM802828", "GSM802829", "GSM802830", "GSM802831", "GSM802832", "GSM802833", "GSM802834", "GSM802835", "GSM802836", "GSM802837", "GSM802838", "GSM802839", "GSM802840", "GSM802841", "GSM802842", "GSM802843", "GSM802844", "GSM802845", "GSM802846", "GSM802847", "GSM802848", "GSM802849", "GSM802850", "GSM802851", "GSM802852", "GSM802853", "GSM802854", "GSM802855", "GSM802856", "GSM802857", "GSM802858", "GSM802859", "GSM802860", "GSM802861", "GSM802862", "GSM802863", "GSM802864", "GSM802865", "GSM802866", "GSM802867", "GSM802868", "GSM802869", "GSM802870", "GSM802871", "GSM802872", "GSM802873", "GSM802874", "GSM802875", "GSM802876", "GSM802877", "GSM802878", "GSM802879", "GSM802880", "GSM802881", "GSM802882", "GSM802883", "GSM802884", "GSM802885", "GSM802886"], "sample_count": 80, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "CPDR tumor-benign 80 genechip dataset", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE32571", "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=GSE32571", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32571", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM807224", "GSM807225", "GSM807226", "GSM807227", "GSM807228", "GSM807229", "GSM807230", "GSM807231", "GSM807232", "GSM807233", "GSM807234", "GSM807235", "GSM807236", "GSM807237", "GSM807238", "GSM807239", "GSM807240", "GSM807241", "GSM807242", "GSM807243", "GSM807244", "GSM807245", "GSM807246", "GSM807247", "GSM807248", "GSM807249", "GSM807250", "GSM807251", "GSM807252", "GSM807253", "GSM807254", "GSM807255", "GSM807256", "GSM807257", "GSM807258", "GSM807259", "GSM807260", "GSM807261", "GSM807262", "GSM807263", "GSM807264", "GSM807265", "GSM807266", "GSM807267", "GSM807268", "GSM807269", "GSM807270", "GSM807271", "GSM807272", "GSM807273", "GSM807274", "GSM807275", "GSM807276", "GSM807277", "GSM807278", "GSM807279", "GSM807280", "GSM807281", "GSM807282", "GSM807283", "GSM807284", "GSM807285", "GSM807286", "GSM807287", "GSM807288", "GSM807289", "GSM807290", "GSM807291", "GSM807292", "GSM807293", "GSM807294", "GSM807295", "GSM807296", "GSM807297", "GSM807298", "GSM807299", "GSM807300", "GSM807301", "GSM807302", "GSM807303", "GSM807304", "GSM807305", "GSM807306", "GSM807307", "GSM807308", "GSM807309", "GSM807310", "GSM807311", "GSM807312", "GSM807313", "GSM807314", "GSM807315", "GSM807316", "GSM807317", "GSM807318", "GSM807319", "GSM807320", "GSM807321"], "sample_count": 98, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Gene signatures in prostate cancer linked to the Gleason score", "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:GSE46602", "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=GSE46602", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE46602", "version": null, "note": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1133136", "GSM1133137", "GSM1133138", "GSM1133139", "GSM1133140", "GSM1133141", "GSM1133142", "GSM1133143", "GSM1133144", "GSM1133145", "GSM1133146", "GSM1133147", "GSM1133148", "GSM1133149", "GSM1133150", "GSM1133151", "GSM1133152", "GSM1133153", "GSM1133154", "GSM1133155", "GSM1133156", "GSM1133157", "GSM1133158", "GSM1133159", "GSM1133160", "GSM1133161", "GSM1133162", "GSM1133163", "GSM1133164", "GSM1133165", "GSM1133166", "GSM1133167", "GSM1133168", "GSM1133169", "GSM1133170", "GSM1133171", "GSM1133172", "GSM1133173", "GSM1133174", "GSM1133175", "GSM1133176", "GSM1133177", "GSM1133178", "GSM1133179", "GSM1133180", "GSM1133181", "GSM1133182", "GSM1133183", "GSM1133184", "GSM1133185"], "sample_count": 50, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from prostate cancer and benign prostate glands", "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:GSE32448 not downloaded", "asset:data:geo:GSE32448 licence not read", "asset:data:geo:GSE32571 not downloaded", "asset:data:geo:GSE32571 licence not read", "asset:data:geo:GSE46602 not downloaded", "asset:data:geo:GSE46602 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "log_rank_test", "label": "Survival analysis", "dsl_operations": ["logrank_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The Kaplan–Meier method with the log-rank test was applied to compare the overall survival for different IFITM1 patterns."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "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": 0.7, "band": "medium", "quote": "limma"}}, {"id": "method-4", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-5", "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"}}], "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": ["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": ["GSE32571", "GSE32448", "GSE46602"], "resolved_accessions": ["GSE32571", "GSE32448", "GSE46602"], "statements": ["The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author."], "basis": "The paper names GSE32571, GSE32448, GSE46602 in 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:36591519", "data:geo:GSE32448"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE32448"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:22:08Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12542, "completion_tokens": 1651, "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:36591519", "type": "paper", "label": "pmid:36591519"}, {"id": "source:pmid:36591519", "type": "manuscript", "label": "PMID 36591519 full text"}, {"id": "data:geo:GSE32448", "type": "dataset", "label": "GEO GSE32448"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36591519", "type": "paper", "label": "pmid:36591519"}, {"id": "source:pmid:36591519", "type": "manuscript", "label": "PMID 36591519 full text"}, {"id": "data:geo:GSE32448", "type": "dataset", "label": "GEO GSE32448"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36591519", "type": "extraction", "used": ["source:pmid:36591519"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE32448", "type": "accession_resolution", "used": ["data:geo:GSE32448"], "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:36591519", "parent_hash": "sha256:fcc52330ab780d276170ebcdcce42e113d5e7e728263a1cedc45e8ea7c165dbd", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE32448 licence not read", "asset:data:geo:GSE32448 not downloaded", "asset:data:geo:GSE32571 licence not read", "asset:data:geo:GSE32571 not downloaded", "asset:data:geo:GSE46602 licence not read", "asset:data:geo:GSE46602 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": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["om the American Type Culture Collection. The cell lines were cultured in RPMI-1640 medium (Gibco, United States).", "Type Culture Collection. The cell lines were cultured in RPMI-1640 medium (Gibco, United States). All"], "order_basis": "paper_text_order:4013", "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": ["The Kaplan–Meier method with the log-rank test was applied to compare the overall survival for different IFITM1 patterns."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}