Integrated bioinformatics analysis identifies PCSK9 as a prognosticator correlated with lipid metabolism in pancreatic adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39342295", "kind": "science-record", "revision": 4, "content_hash": "sha256:5ba4c3f7ab146cc7fa342bd8aceebdb201e59afd09822e8e420e2226aaf6bd80", "created_at": "2026-11-01T20:29:32Z", "updated_at": "2026-11-01T22:55:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated bioinformatics analysis identifies PCSK9 as a prognosticator correlated with lipid metabolism in pancreatic adenocarcinoma.", "doi": "10.1186/s12957-024-03532-0", "pmid": "39342295", "authors": ["Siqi Zhou", "Qiyuan Guo", "Aotian Chen", "Xihan Li", "Xiaoping Zou"], "journal": "World journal of surgical oncology", "year": 2024, "abstract": "BACKGROUND: Pancreatic adenocarcinoma (PAAD) is the most frequent kind of pancreatic cancer (PC). Recent studies suggest that lipid metabolism facilitates tumorigenesis, disease progression, and resistance to therapy by promoting lipid synthesis, accumulation, and breakdown. Thus, exploring the lipid metabolism network could unveil novel therapeutic avenues for early detection, precision medicine, and prognostication in PAAD. This project intends to develop new lipid metabolism-related biomarkers for PAAD diagnosis and investigate the link between important genes and immune cell infiltration (ICI).\nMETHODS: Tissue samples from 20 PAAD patients and 20 healthy controls were obtained. Analysis were focused on the datasets GSE71729 and GSE16515, which include samples of PAAD (n = 161) and those from healthy human tissue (n = 61), derived from the GEO database. Knockdown of PCSK9 on PC cells were conducted by si-RNA and sh-RNA. Migration and cell functional experiments were performed to assess the role of PCSK9 in cell multiplication. Furthermore, a xenograft mouse model was employed to confirm PCSK9's function in vivo.\nRESULTS: The expression level of Proprotein convertase subtilisin/kexin type 9 (PCSK9) is significantly elevated in tissues affected by PAAD when compared to normal tissues. Survival analyses indicated that increased PCSK9 levels are inversely related to overall and disease-free survival (DFS). PCSK9's functional annotation associated it with the cell cycle and metabolism, especially energy metabolism. Examination of ICI data determined that PCSK9 expression demonstrated an unambiguous association with the M0 macrophages, T follicular helper cells (Tfh), gamma delta T cells and activated DC, and an inverse relationship with Monocytes, CD8+ T cells, memory B cells, resting CD4+ memory T cells, activated NK cells and resting DC abundance. PCSK9 expression knockdown has the ability to impede PC cells' migration and proliferation.\nCONCLUSION: Our study identified PCSK9 as a critical gene in PAAD. Expression levels of PCSK9 varied between PAAD and normal samples. ROC analysis verified PCSK9's strong capacity to differentiate PC from normal samples. Importantly, PCSK9 expression was considerably elevated in PC cell lines and tissues. Furthermore, PCSK9 stimulates the migration and proliferation of tumor cells in vivo and vitro.", "claims": [{"id": "claim-method", "statement": "Two machine learning methods were used to identify important genes from the 20 DELMRGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39342295", "locator": "sections[21] \"Identification of candidate hub genes via machine learning\" paragraph 2", "quote": "Two machine learning methods were used to identify important genes from the 20 DELMRGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this article. The original data can be provided by the corresponding author upon reasonable request.\nNo datasets were generated or analysed during the current study.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39342295", "locator": "sections[44] \"Data Availability Statement\" paragraphs 1-3", "quote": "All data generated or analyzed during this study are included in this article. The original data can be provided by the corresponding author upon reasonable request.\nNo datasets were generated or analysed during the current study."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified PCSK9 as a critical gene in PAAD.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39342295", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "Our study identified PCSK9 as a critical gene in PAAD."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study identified PCSK9 as a critical gene in PAAD.", "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:39342295"], "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:GSE15471"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:machine_learning_random_forest", "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:GSE15471"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:machine_learning_random_forest"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39342295", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12957-024-03532-0", "sha256": "sha256:a0eed590990a42711b3d9d25e3b80dac03abfb364f753a0c14a7a23a070cf9b5", "bytes": 38115, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12957-024-03532-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11439283", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15471", "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=GSE15471", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15471", "version": null, "note": "All data generated or analyzed during this study are included in this article. The original data can be provided by the corresponding author upon reasonable request.\nNo datasets were generated or analysed during the current study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this article. The original data can be provided by the corresponding author upon reasonable request.\nNo datasets were generated or analysed during the current study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM388076", "GSM388077", "GSM388078", "GSM388079", "GSM388080", "GSM388081", "GSM388082", "GSM388083", "GSM388084", "GSM388085", "GSM388086", "GSM388087", "GSM388088", "GSM388089", "GSM388090", "GSM388091", "GSM388092", "GSM388093", "GSM388094", "GSM388095", "GSM388096", "GSM388097", "GSM388098", "GSM388099", "GSM388100", "GSM388101", "GSM388102", "GSM388103", "GSM388104", "GSM388105", "GSM388106", "GSM388107", "GSM388108", "GSM388109", "GSM388110", "GSM388111", "GSM388112", "GSM388113", "GSM388114", "GSM388115", "GSM388116", "GSM388117", "GSM388118", "GSM388119", "GSM388120", "GSM388121", "GSM388122", "GSM388123", "GSM388124", "GSM388125", "GSM388126", "GSM388127", "GSM388128", "GSM388129", "GSM388130", "GSM388131", "GSM388132", "GSM388133", "GSM388134", "GSM388135", "GSM388136", "GSM388137", "GSM388138", "GSM388139", "GSM388140", "GSM388141", "GSM388142", "GSM388143", "GSM388144", "GSM388145", "GSM388146", "GSM388147", "GSM388148", "GSM388149", "GSM388150", "GSM388151", "GSM388152", "GSM388153"], "sample_count": 78, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Whole-Tissue Gene Expression Study of Pancreatic Ductal Adenocarcinoma", "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:GSE16515", "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=GSE16515", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16515", "version": null, "note": "All data generated or analyzed during this study are included in this article. The original data can be provided by the corresponding author upon reasonable request.\nNo datasets were generated or analysed during the current study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this article. The original data can be provided by the corresponding author upon reasonable request.\nNo datasets were generated or analysed during the current study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM414924", "GSM414925", "GSM414926", "GSM414927", "GSM414928", "GSM414929", "GSM414930", "GSM414931", "GSM414932", "GSM414933", "GSM414934", "GSM414935", "GSM414936", "GSM414937", "GSM414938", "GSM414939", "GSM414940", "GSM414941", "GSM414942", "GSM414943", "GSM414944", "GSM414945", "GSM414946", "GSM414947", "GSM414948", "GSM414949", "GSM414950", "GSM414951", "GSM414952", "GSM414953", "GSM414954", "GSM414955", "GSM414956", "GSM414957", "GSM414958", "GSM414959", "GSM414960", "GSM414961", "GSM414962", "GSM414963", "GSM414964", "GSM414965", "GSM414966", "GSM414967", "GSM414968", "GSM414969", "GSM414970", "GSM414971", "GSM414972", "GSM414973", "GSM414974", "GSM414975"], "sample_count": 52, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from Mayo Clinic Pancreatic Tumor and Normal 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:GSE71729", "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=GSE71729", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE71729", "version": null, "note": "All data generated or analyzed during this study are included in this article. The original data can be provided by the corresponding author upon reasonable request.\nNo datasets were generated or analysed during the current study.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this article. The original data can be provided by the corresponding author upon reasonable request.\nNo datasets were generated or analysed during the current study.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1843893", "GSM1843894", "GSM1843895", "GSM1843896", "GSM1843897", "GSM1843898", "GSM1843899", "GSM1843900", "GSM1843901", "GSM1843902", "GSM1843903", "GSM1843904", "GSM1843905", "GSM1843906", "GSM1843907", "GSM1843908", "GSM1843909", "GSM1843910", "GSM1843911", "GSM1843912", "GSM1843913", "GSM1843914", "GSM1843915", "GSM1843916", "GSM1843917", "GSM1843918", "GSM1843919", "GSM1843920", "GSM1843921", "GSM1843922", "GSM1843923", "GSM1843924", "GSM1843925", "GSM1843926", "GSM1843927", "GSM1843928", "GSM1843929", "GSM1843930", "GSM1843931", "GSM1843932", "GSM1843933", "GSM1843934", "GSM1843935", "GSM1843936", "GSM1843937", "GSM1843938", "GSM1843939", "GSM1843940", "GSM1843941", "GSM1843942", "GSM1843943", "GSM1843944", "GSM1843945", "GSM1843946", "GSM1843947", "GSM1843948", "GSM1843949", "GSM1843950", "GSM1843951", "GSM1843952", "GSM1843953", "GSM1843954", "GSM1843955", "GSM1843956", "GSM1843957", "GSM1843958", "GSM1843959", "GSM1843960", "GSM1843961", "GSM1843962", "GSM1843963", "GSM1843964", "GSM1843965", "GSM1843966", "GSM1843967", "GSM1843968", "GSM1843969", "GSM1843970", "GSM1843971", "GSM1843972", "GSM1843973", "GSM1843974", "GSM1843975", "GSM1843976", "GSM1843977", "GSM1843978", "GSM1843979", "GSM1843980", "GSM1843981", "GSM1843982", "GSM1843983", "GSM1843984", "GSM1843985", "GSM1843986", "GSM1843987", "GSM1843988", "GSM1843989", "GSM1843990", "GSM1843991", "GSM1843992", "GSM1843993", "GSM1843994", "GSM1843995", "GSM1843996", "GSM1843997", "GSM1843998", "GSM1843999", "GSM1844000", "GSM1844001", "GSM1844002", "GSM1844003", "GSM1844004", "GSM1844005", "GSM1844006", "GSM1844007", "GSM1844008", "GSM1844009", "GSM1844010", "GSM1844011", "GSM1844012", "GSM1844013", "GSM1844014", "GSM1844015", "GSM1844016", "GSM1844017", "GSM1844018", "GSM1844019", "GSM1844020", "GSM1844021", "GSM1844022", "GSM1844023", "GSM1844024", "GSM1844025", "GSM1844026", "GSM1844027", "GSM1844028", "GSM1844029", "GSM1844030", "GSM1844031", "GSM1844032", "GSM1844033", "GSM1844034", "GSM1844035", "GSM1844036", "GSM1844037", "GSM1844038", "GSM1844039", "GSM1844040", "GSM1844041", "GSM1844042", "GSM1844043", "GSM1844044", "GSM1844045", "GSM1844046", "GSM1844047", "GSM1844049", "GSM1844050", "GSM1844051", "GSM1844052", "GSM1844053", "GSM1844054", "GSM1844055", "GSM1844056", "GSM1844057", "GSM1844058", "GSM1844059", "GSM1844060", "GSM1844061", "GSM1844062", "GSM1844063", "GSM1844064", "GSM1844065", "GSM1844066", "GSM1844067", "GSM1844068", "GSM1844069", "GSM1844070", "GSM1844071", "GSM1844072", "GSM1844073", "GSM1844074", "GSM1844075", "GSM1844076", "GSM1844077", "GSM1844078", "GSM1844079", "GSM1844080", "GSM1844081", "GSM1844082", "GSM1844083", "GSM1844084", "GSM1844085", "GSM1844086", "GSM1844088", "GSM1844089", "GSM1844090", "GSM1844091", "GSM1844092", "GSM1844093", "GSM1844094", "GSM1844095", "GSM1844096", "GSM1844097", "GSM1844098", "GSM1844099", "GSM1844100", "GSM1844101", "GSM1844102", "GSM1844103", "GSM1844104", "GSM1844105", "GSM1844106", "GSM1844107", "GSM1844108", "GSM1844109", "GSM1844110", "GSM1844111", "GSM1844112", "GSM1844113", "GSM1844114", "GSM1844115", "GSM1844116", "GSM1844117", "GSM1844118", "GSM1844119", "GSM1844120", "GSM1844121", "GSM1844122", "GSM1844123", "GSM1844124", "GSM1844125", "GSM1844126", "GSM1844127", "GSM1844128", "GSM1844129", "GSM1844130", "GSM1844131", "GSM1844132", "GSM1844133", "GSM1844134", "GSM1844135", "GSM1844136", "GSM1844137", "GSM1844138", "GSM1844139", "GSM1844140", "GSM1844141", "GSM1844142", "GSM1844143", "GSM1844144", "GSM1844145", "GSM1844146", "GSM1844147", "GSM1844148", "GSM1844149", "GSM1844150", "GSM1844151", "GSM1844152", "GSM1844153", "GSM1844154", "GSM1844155", "GSM1844156", "GSM1844157", "GSM1844158", "GSM1844159", "GSM1844160", "GSM1844161", "GSM1844162", "GSM1844163", "GSM1844164", "GSM1844165", "GSM1844166", "GSM1844167", "GSM1844168", "GSM1844169", "GSM1844170", "GSM1844171", "GSM1844172", "GSM1844173", "GSM1844174", "GSM1844175", "GSM1844176", "GSM1844177", "GSM1844178", "GSM1844179", "GSM1844180", "GSM1844181", "GSM1844182", "GSM1844183", "GSM1844184", "GSM1844185", "GSM1844186", "GSM1844187", "GSM1844188", "GSM1844189", "GSM1844190", "GSM1844191", "GSM1844192", "GSM1844193", "GSM1844194", "GSM1844195", "GSM1844196", "GSM1844197", "GSM1844198", "GSM1844199", "GSM1844200", "GSM1844201", "GSM1844202", "GSM1844203", "GSM1844204", "GSM1844205", "GSM1844206", "GSM1844207", "GSM1844208", "GSM1844209", "GSM1844210", "GSM1844211", "GSM1844212", "GSM1844213", "GSM1844214", "GSM1844215", "GSM1844216", "GSM1844217", "GSM1844218", "GSM1844219", "GSM1844220", "GSM1844221", "GSM1844222", "GSM1844223", "GSM1844224", "GSM1844225", "GSM1844226", "GSM1844227", "GSM1844228", "GSM1844229", "GSM1844230", "GSM1844231", "GSM1844232", "GSM1844233", "GSM1844234", "GSM1844235", "GSM1844236", "GSM1844237", "GSM1844238", "GSM1844239", "GSM1844240", "GSM1844241", "GSM1844242", "GSM1844243", "GSM1844244", "GSM1844245", "GSM1844246", "GSM1844247", "GSM1844248", "GSM1844249", "GSM1844250", "GSM1844251"], "sample_count": 357, "group_sizes": null, "group_sizes_basis": null, "platform": "20769", "taxon": "Homo sapiens", "title": "Virtual Microdissection of Pancreatic Ductal Adenocarcinoma Reveals Tumor and Stroma Subtypes.", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE15471 not downloaded", "asset:data:geo:GSE15471 licence not read", "asset:data:geo:GSE16515 not downloaded", "asset:data:geo:GSE16515 licence not read", "asset:data:geo:GSE71729 not downloaded", "asset:data:geo:GSE71729 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "machine_learning", "specific": "random_forest", "label": "Machine learning", "dsl_operations": [], "missing_operations": ["machine_learning_random_forest"], "expressible": false, "parameters": {}, "data_shapes": ["labelled_feature_matrix"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Two machine learning methods were used to identify important genes from the 20 DELMRGs."}}, {"id": "method-2", "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": 0.7, "band": "medium", "quote": "ROC analysis"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor", "method.machine_learning_random_forest"]}, "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": false, "required_operations": [], "missing_operations": ["machine_learning_random_forest"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: random_forest."}, "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": ["GSE71729", "GSE16515", "GSE15471"], "resolved_accessions": ["GSE71729", "GSE16515", "GSE15471"], "statements": ["All data generated or analyzed during this study are included in this article. The original data can be provided by the corresponding author upon reasonable request.\nNo datasets were generated or analysed during the current study."], "basis": "The paper names GSE71729, GSE16515, GSE15471 in GEO database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:39342295", "data:geo:GSE15471"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "machine_learning_random_forest", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE15471"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:33:27Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 10929, "completion_tokens": 1895, "cached_tokens": 128}}, "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:39342295", "type": "paper", "label": "pmid:39342295"}, {"id": "source:pmid:39342295", "type": "manuscript", "label": "PMID 39342295 full text"}, {"id": "data:geo:GSE15471", "type": "dataset", "label": "GEO GSE15471"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39342295", "type": "paper", "label": "pmid:39342295"}, {"id": "source:pmid:39342295", "type": "manuscript", "label": "PMID 39342295 full text"}, {"id": "data:geo:GSE15471", "type": "dataset", "label": "GEO GSE15471"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39342295", "type": "extraction", "used": ["source:pmid:39342295"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE15471", "type": "accession_resolution", "used": ["data:geo:GSE15471"], "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:39342295", "parent_hash": "sha256:7827a63196e55937f960e4604bd9e92e9986b08c84a564eb0df3e2a5dde93c98", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE15471 licence not read", "asset:data:geo:GSE15471 not downloaded", "asset:data:geo:GSE16515 licence not read", "asset:data:geo:GSE16515 not downloaded", "asset:data:geo:GSE71729 licence not read", "asset:data:geo:GSE71729 not downloaded", "execution.not_run", "method.machine_learning_random_forest", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:machine_learning_random_forest"], "assays": [{"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["sue (n = 61), derived from the GEO database. Knockdown of PCSK9 on PC cells were conducted by si-RN", "s and resting DC abundance. PCSK9 expression knockdown has the ability to impede PC cells' migratio"], "order_basis": "paper_text_order:959", "id": "assay:1"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ell multiplication. Furthermore, a xenograft mouse model was employed to confirm PCSK9's function in", "del was employed to confirm PCSK9's function in vivo. RESULTS: The expression level of Proprotein", "e migration and proliferation of tumor cells in vivo and vitro.", "ell multiplication. Furthermore, a xenograft mouse model was employed to confirm PCSK9's functi"], "order_basis": "paper_text_order:1161", "id": "assay:2"}, {"role": "analysis", "definition_id": "machine_learning", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Two machine learning methods were used to identify important genes from the 20 DELMRGs."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}