Identification of a chemoresistance-related prognostic gene signature by comprehensive analysis and experimental validation in pancreatic cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37251940", "kind": "science-record", "revision": 3, "content_hash": "sha256:07d3f6f9a5d1790134d8bb1499df1105526779ee74929158dac8488fee871f37", "created_at": "2026-11-01T19:01:58Z", "updated_at": "2026-11-01T22:09:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a chemoresistance-related prognostic gene signature by comprehensive analysis and experimental validation in pancreatic cancer.", "doi": "10.3389/fonc.2023.1132424", "pmid": "37251940", "authors": ["Junliang Chen", "Zhihao Liu", "Zhiyuan Wu", "Wenjun Li", "Xiaodong Tan"], "journal": "Frontiers in oncology", "year": 2023, "abstract": "Background: Chemoresistance is a major hurdle to improving the prognosis of pancreatic cancer (PC). This study aimed to identify key genes regulating chemoresistance and develop a chemoresistance-related gene signature for prognosis prediction.\nMethods: A total of 30 PC cell lines were subtyped according to gemcitabine sensitivity data from the Cancer Therapeutics Response Portal (CTRP v2). Differentially expressed genes (DEGs) between gemcitabine-resistant and gemcitabine-sensitive cells were subsequently identified. These upregulated DEGs associated with prognostic values were incorporated to build a LASSO Cox risk model for The Cancer Genome Atlas (TCGA) cohort. Four datasets (GSE28735, GSE62452, GSE85916, and GSE102238) from the Gene Expression Omnibus (GEO) were used as an external validation cohort. Then, a nomogram was developed based on independent prognostic factors. The responses to multiple anti-PC chemotherapeutics were estimated by the \"oncoPredict\" method. Tumor mutation burden (TMB) was calculated using the \"TCGAbiolinks\" package. Analysis of the tumor microenvironment (TME) was performed using the \"IOBR\" package, while the TIDE and \"easier\" algorithms were employed to estimate immunotherapy efficacy. Finally, RT-qPCR, Western blot and CCK-8 assays were conducted to validate the expression and functions of ALDH3B1 and NCEH1.\nResults: A five-gene signature and a predictive nomogram were developed from six prognostic DEGs, including EGFR, MSLN, ERAP2, ALDH3B1, and NCEH1. Bulk and single-cell RNA sequencing analyses indicated that all five genes were highly expressed in tumor samples. This gene signature was not only an independent prognostic factor but also a biomarker forecasting chemoresistance, TMB, and immune cells. In vitro experiments suggested that ALDH3B1 and NCEH1 were involved in PC progression and gemcitabine chemoresistance.\nConclusion: This chemoresistance-related gene signature links prognosis with chemoresistance, TMB, and immune features. ALDH3B1 and NCEH1 are two promising targets for treating PC.", "claims": [{"id": "claim-method", "statement": "The least absolute shrinkage and selection operator (LASSO) Cox regression algorithm was applied to develop a risk model from the prognostic genes associated with chemoresistance in the TCGA cohort (16).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37251940", "locator": "sections[5] \"Risk model development and evaluation\" paragraph 2", "quote": "The least absolute shrinkage and selection operator (LASSO) Cox regression algorithm was applied to develop a risk model from the prognostic genes associated with chemoresistance in the TCGA cohort (16)."}], "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:37251940", "locator": "sections[24] \"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"}, {"id": "claim-target-result", "statement": "A five-gene signature and a predictive nomogram were developed from six prognostic DEGs, including EGFR, MSLN, ERAP2, ALDH3B1, and NCEH1.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37251940", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A five-gene signature and a predictive nomogram were developed from six prognostic DEGs, including EGFR, MSLN, ERAP2, ALDH3B1, and NCEH1."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A five-gene signature and a predictive nomogram were developed from six prognostic DEGs, including EGFR, MSLN, ERAP2, ALDH3B1, and NCEH1.", "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:37251940"], "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:GSE101448"], "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:GSE101448"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37251940", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fonc.2023.1132424", "sha256": "sha256:547b06894982d16224bd88f9cc0539613578a4609e60f3c42f609221c311e5a1", "bytes": 43175, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fonc.2023.1132424", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10213255", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE101448", "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=GSE101448", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE101448", "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": ["GSM2703750", "GSM2703751", "GSM2703752", "GSM2703753", "GSM2703754", "GSM2703755", "GSM2703756", "GSM2703757", "GSM2703758", "GSM2703759", "GSM2703760", "GSM2703761", "GSM2703762", "GSM2703763", "GSM2703764", "GSM2703765", "GSM2703766", "GSM2703767", "GSM2703768", "GSM2703769", "GSM2703770", "GSM2703771", "GSM2703772", "GSM2703773", "GSM2703774", "GSM2703775", "GSM2703776", "GSM2703777", "GSM2703778", "GSM2703779", "GSM2703780", "GSM2703781", "GSM2703782", "GSM2703783", "GSM2703784", "GSM2703785", "GSM2703786", "GSM2703787", "GSM2703788", "GSM2703789", "GSM2703790", "GSM2703791", "GSM2703792"], "sample_count": 43, "group_sizes": null, "group_sizes_basis": null, "platform": "10558", "taxon": "Homo sapiens", "title": "Microarray gene-expression data to identify a robust biomarker signature in PDAC and validate it in formalin-fixed paraffin-embedded tissue material.", "resolution_checked_at": "2026-11-01T18:06:43Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE102238", "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=GSE102238", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE102238", "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": ["GSM2731543", "GSM2731544", "GSM2731545", "GSM2731546", "GSM2731547", "GSM2731548", "GSM2731549", "GSM2731550", "GSM2731551", "GSM2731552", "GSM2731553", "GSM2731554", "GSM2731555", "GSM2731556", "GSM2731557", "GSM2731558", "GSM2731559", "GSM2731560", "GSM2731561", "GSM2731562", "GSM2731563", "GSM2731564", "GSM2731565", "GSM2731566", "GSM2731567", "GSM2731568", "GSM2731569", "GSM2731570", "GSM2731571", "GSM2731572", "GSM2731573", "GSM2731574", "GSM2731575", "GSM2731576", "GSM2731577", "GSM2731578", "GSM2731579", "GSM2731580", "GSM2731581", "GSM2731582", "GSM2731583", "GSM2731584", "GSM2731585", "GSM2731586", "GSM2731587", "GSM2731588", "GSM2731589", "GSM2731590", "GSM2731591", "GSM2731592", "GSM2731593", "GSM2731594", "GSM2731595", "GSM2731596", "GSM2731597", "GSM2731598", "GSM2731599", "GSM2731600", "GSM2731601", "GSM2731602", "GSM2731603", "GSM2731604", "GSM2731605", "GSM2731606", "GSM2731607", "GSM2731608", "GSM2731609", "GSM2731610", "GSM2731611", "GSM2731612", "GSM2731613", "GSM2731614", "GSM2731615", "GSM2731616", "GSM2731617", "GSM2731618", "GSM2731619", "GSM2731620", "GSM2731621", "GSM2731622", "GSM2731623", "GSM2731624", "GSM2731625", "GSM2731626", "GSM2731627", "GSM2731628", "GSM2731629", "GSM2731630", "GSM2731631", "GSM2731632", "GSM2731633", "GSM2731634", "GSM2731635", "GSM2731636", "GSM2731637", "GSM2731638", "GSM2731639", "GSM2731640", "GSM2731641", "GSM2731642"], "sample_count": 100, "group_sizes": null, "group_sizes_basis": null, "platform": "19072", "taxon": "Homo sapiens", "title": "Gene expression signatures associated with Perineural Invasion in 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:GSE212996", "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=GSE212996", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE212996", "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": ["GSM6568244", "GSM6568245", "GSM6568246", "GSM6568247", "GSM6568248", "GSM6568249", "GSM6568250", "GSM6568251", "GSM6568252", "GSM6568253", "GSM6568254", "GSM6568255", "GSM6568256", "GSM6568257", "GSM6568258", "GSM6568259", "GSM6568260", "GSM6568261", "GSM6568262", "GSM6568263", "GSM6568264", "GSM6568265", "GSM6568266", "GSM6568267", "GSM6568268", "GSM6568269", "GSM6568270"], "sample_count": 27, "group_sizes": null, "group_sizes_basis": null, "platform": "24676;21697;15520", "taxon": "Homo sapiens", "title": "Engineered cell entry links receptor biology with single-cell genomics [scRNA-Seq]", "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:GSE28735", "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=GSE28735", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE28735", "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": ["GSM711904", "GSM711905", "GSM711906", "GSM711907", "GSM711908", "GSM711909", "GSM711910", "GSM711911", "GSM711912", "GSM711913", "GSM711914", "GSM711915", "GSM711916", "GSM711917", "GSM711918", "GSM711919", "GSM711920", "GSM711921", "GSM711922", "GSM711923", "GSM711924", "GSM711925", "GSM711926", "GSM711927", "GSM711928", "GSM711929", "GSM711930", "GSM711931", "GSM711932", "GSM711933", "GSM711934", "GSM711935", "GSM711936", "GSM711937", "GSM711938", "GSM711939", "GSM711940", "GSM711941", "GSM711942", "GSM711943", "GSM711944", "GSM711945", "GSM711946", "GSM711947", "GSM711948", "GSM711949", "GSM711950", "GSM711951", "GSM711952", "GSM711953", "GSM711954", "GSM711955", "GSM711956", "GSM711957", "GSM711958", "GSM711959", "GSM711960", "GSM711961", "GSM711962", "GSM711963", "GSM711964", "GSM711965", "GSM711966", "GSM711967", "GSM711968", "GSM711969", "GSM711970", "GSM711971", "GSM711972", "GSM711973", "GSM711974", "GSM711975", "GSM711976", "GSM711977", "GSM711978", "GSM711979", "GSM711980", "GSM711981", "GSM711982", "GSM711983", "GSM711984", "GSM711985", "GSM711986", "GSM711987", "GSM711988", "GSM711989", "GSM711990", "GSM711991", "GSM711992", "GSM711993"], "sample_count": 90, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Microarray gene-expression profiles of 45 matching pairs of pancreatic tumor and adjacent non-tumor tissues from 45 patients with 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:GSE62452", "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=GSE62452", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE62452", "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": ["GSM1527105", "GSM1527106", "GSM1527107", "GSM1527108", "GSM1527109", "GSM1527110", "GSM1527111", "GSM1527112", "GSM1527113", "GSM1527114", "GSM1527115", "GSM1527116", "GSM1527117", "GSM1527118", "GSM1527119", "GSM1527120", "GSM1527121", "GSM1527122", "GSM1527123", "GSM1527124", "GSM1527125", "GSM1527126", "GSM1527127", "GSM1527128", "GSM1527129", "GSM1527130", "GSM1527131", "GSM1527132", "GSM1527133", "GSM1527134", "GSM1527135", "GSM1527136", "GSM1527137", "GSM1527138", "GSM1527139", "GSM1527140", "GSM1527141", "GSM1527142", "GSM1527143", "GSM1527144", "GSM1527145", "GSM1527146", "GSM1527147", "GSM1527148", "GSM1527149", "GSM1527150", "GSM1527151", "GSM1527152", "GSM1527153", "GSM1527154", "GSM1527155", "GSM1527156", "GSM1527157", "GSM1527158", "GSM1527159", "GSM1527160", "GSM1527161", "GSM1527162", "GSM1527163", "GSM1527164", "GSM1527165", "GSM1527166", "GSM1527167", "GSM1527168", "GSM1527169", "GSM1527170", "GSM1527171", "GSM1527172", "GSM1527173", "GSM1527174", "GSM1527175", "GSM1527176", "GSM1527177", "GSM1527178", "GSM1527179", "GSM1527180", "GSM1527181", "GSM1527182", "GSM1527183", "GSM1527184", "GSM1527185", "GSM1527186", "GSM1527187", "GSM1527188", "GSM1527189", "GSM1527190", "GSM1527191", "GSM1527192", "GSM1527193", "GSM1527194", "GSM1527195", "GSM1527196", "GSM1527197", "GSM1527198", "GSM1527199", "GSM1527200", "GSM1527201", "GSM1527202", "GSM1527203", "GSM1527204", "GSM1527205", "GSM1527206", "GSM1527207", "GSM1527208", "GSM1527209", "GSM1527210", "GSM1527211", "GSM1527212", "GSM1527213", "GSM1527214", "GSM1527215", "GSM1527216", "GSM1527217", "GSM1527218", "GSM1527219", "GSM1527220", "GSM1527221", "GSM1527222", "GSM1527223", "GSM1527224", "GSM1527225", "GSM1527226", "GSM1527227", "GSM1527228", "GSM1527229", "GSM1527230", "GSM1527231", "GSM1527232", "GSM1527233", "GSM1527234"], "sample_count": 130, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Microarray gene-expression profiles of 69 pancreatic tumors and 61 adjacent non-tumor tissue from patients with pancreatic ductal adenocarcinoma", "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:GSE101448 not downloaded", "asset:data:geo:GSE101448 licence not read", "asset:data:geo:GSE102238 not downloaded", "asset:data:geo:GSE102238 licence not read", "asset:data:geo:GSE212996 not downloaded", "asset:data:geo:GSE212996 licence not read", "asset:data:geo:GSE28735 not downloaded", "asset:data:geo:GSE28735 licence not read", "asset:data:geo:GSE62452 not downloaded", "asset:data:geo:GSE62452 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The least absolute shrinkage and selection operator (LASSO) Cox regression algorithm was applied to develop a risk model from the prognostic genes associated with chemoresistance in the TCGA cohort (16)."}}, {"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"}}], "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": ["cox_ph"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: cox_proportional_hazards."}, "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": ["GSE28735", "GSE62452", "GSE85916 and GSE102238", "GSE97003 and GSE181625", "GSE212996", "GSE102238", "GSE101448"], "resolved_accessions": ["GSE28735", "GSE62452", "GSE212996", "GSE102238", "GSE101448"], "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 GSE28735, GSE62452, GSE212996, GSE102238, GSE101448 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": ["cox_ph"], "assets": ["source:pmid:37251940", "data:geo:GSE101448"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE101448"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:42:27Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12113, "completion_tokens": 3056, "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:37251940", "type": "paper", "label": "pmid:37251940"}, {"id": "source:pmid:37251940", "type": "manuscript", "label": "PMID 37251940 full text"}, {"id": "data:geo:GSE101448", "type": "dataset", "label": "GEO GSE101448"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37251940", "type": "paper", "label": "pmid:37251940"}, {"id": "source:pmid:37251940", "type": "manuscript", "label": "PMID 37251940 full text"}, {"id": "data:geo:GSE101448", "type": "dataset", "label": "GEO GSE101448"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37251940", "type": "extraction", "used": ["source:pmid:37251940"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE101448", "type": "accession_resolution", "used": ["data:geo:GSE101448"], "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:37251940", "parent_hash": "sha256:df21079dda10897482daaafd79f4a057e8a7773e31743b7d5588ab7316dd74dc", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE101448 licence not read", "asset:data:geo:GSE101448 not downloaded", "asset:data:geo:GSE102238 licence not read", "asset:data:geo:GSE102238 not downloaded", "asset:data:geo:GSE212996 licence not read", "asset:data:geo:GSE212996 not downloaded", "asset:data:geo:GSE28735 licence not read", "asset:data:geo:GSE28735 not downloaded", "asset:data:geo:GSE62452 licence not read", "asset:data:geo:GSE62452 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": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["to estimate immunotherapy efficacy. Finally, RT-qPCR, Western blot and CCK-8 assays were conducte", "estimate immunotherapy efficacy. Finally, RT-qPCR, Western blot and CCK-8 assays were conducte"], "order_basis": "paper_text_order:1346", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["te immunotherapy efficacy. Finally, RT-qPCR, Western blot and CCK-8 assays were conducted to validate"], "order_basis": "paper_text_order:1355", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["efficacy. Finally, RT-qPCR, Western blot and CCK-8 assays were conducted to validate the expres"], "order_basis": "paper_text_order:1372", "id": "assay:3"}, {"role": "data_generation", "definition_id": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["R, MSLN, ERAP2, ALDH3B1, and NCEH1. Bulk and single-cell RNA sequencing analyses indicated that all five genes were"], "order_basis": "paper_text_order:1619", "id": "assay:4"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["P2, ALDH3B1, and NCEH1. Bulk and single-cell RNA sequencing analyses indicated that all five genes were"], "order_basis": "paper_text_order:1631", "id": "assay:5"}, {"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": ["rials and methods Cell culture and transient transfection Three human pancreatic cancer cell lines (As", "2. Cells in six-well plates were transiently transfected with siRNA using Lipofectamine™ 3000 transfe", "sfected with siRNA using Lipofectamine™ 3000 transfection reagent (Invitrogen, Carlsbad, CA, USA) acco", "ell plates were transiently transfected with siRNA using Lipofectamine™ 3000 transfection reage"], "order_basis": "paper_text_order:2213", "id": "assay:6"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["cox_ph"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The least absolute shrinkage and selection operator (LASSO) Cox regression algorithm was applied to develop a risk model from the prognostic genes associated with chemoresistance in the TCGA cohort (16)."], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}