Single-cell data revealed CD14-type and FCGR3A-type macrophages and relevant prognostic factors for predicting immunotherapy and prognosis in stomach adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38274323", "kind": "science-record", "revision": 3, "content_hash": "sha256:9422dcfca728a3443b739f2e598a0b03ba414ae8d0c1955ed79cfebc54119623", "created_at": "2026-11-01T19:20:12Z", "updated_at": "2026-11-01T22:11:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Single-cell data revealed CD14-type and FCGR3A-type macrophages and relevant prognostic factors for predicting immunotherapy and prognosis in stomach adenocarcinoma.", "doi": "10.7717/peerj.16776", "pmid": "38274323", "authors": ["Mengling Li", "Ming Lu", "Jun Li", "Qingqing Gui", "Yibin Xia", "Chao Lu", "Hongchun Shu"], "journal": "PeerJ", "year": 2024, "abstract": "Background: Stomach adenocarcinoma (STAD) exhibits profound tumor heterogeneity and represents a great therapeutic challenge. Single-cell sequencing technology is a powerful tool to identify characteristic cell types.\nMethods: Single-cell sequencing data (scRNA-seq) GSE167297 and bulk RNA-seq data from TCGA, GTEx, GSE26901 and GSE15459 database were included in this study. By downscaling and annotating the cellular data in scRNA-seq, critical cell types in tumor progression were identified by AUCell score. Relevant gene modules were then identified by weighted gene co-expression network analysis (WGCNA). A prognostic scoring system was constructed by identifying prognostic factors in STAD by Least absolute shrinkage and selection operator (LASSO) COX model. The prognosis and model performance in the RiskScore groups were measured by Kaplan-Meier (K-M) curves and Receiver operating characteristic (ROC) curves. Nomogram was drawn based on RiskScore and prognosis-related clinical factors. In addition, we evaluated patient's feedback on immunotherapy in the RiskScore groups by TIMER, ESTIMATE and TIDE analysis. Finally, the expression levels of prognostic factors were verified in gastric cancer cell lines (MKN7 and MKN28) and human normal gastric mucosal epithelial cells (GES-1), and the effects of prognostic factors on the viability of gastric cancer cells were examined by the CCK8 assay and cell cycle.\nResults: scRNA-seq analysis revealed that 11 cell types were identified, and macrophages exhibited relatively higher AUCell scores and specifically expressed CD14 and FCGR3A. High macrophage scores worsened the prognosis of STAD patients. We intersected the specifically expressed genes in macrophages subgroups (670) and macrophage module genes (2,360) obtained from WGCNA analysis. Among 86 common genes, seven prognostic factors (RGS2, GNAI2, ANXA5, MARCKS, CD36, NRP1 and PDE4A) were identified and composed a RiskScore model. Patients in low Risk group showed a better survival advantage. Nomogram also provided a favorable prediction for survival at 1, 3 and 5 years in STAD patients. Besides, we found positive feedback to immunotherapy in patients with low RiskScore. The expression tendency of the seven prognostic factors in MKN7 and MKN28 was consistent with that in the RNA-seq data in addition to comparison of protein expression levels in the public HPA (The Human Protein Atlas) database. Further functional exploration disclosed that MARCKS was an important prognostic factor in regulating cell viability in STAD.\nConclusion: This study preliminary uncovered a single cell atlas for STAD patients, and Macrophages relevant gene signature and nomogram displayed favorable immunotherapy and prognostic prediction ability. Collectively, our work provides a new insight into the molecular mechanisms and therapeutic approach for LUAD patients.", "claims": [{"id": "claim-method", "statement": "The model was trained based on 5-fold cross-validation to select the penalty parameter λ.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38274323", "locator": "sections[8] \"STAD prognostic system\" paragraph 2", "quote": "The model was trained based on 5-fold cross-validation to select the penalty parameter λ."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:The data is available at NCBI GEO: GSE167297, GSE26901, GSE15459and the raw measurements are available at GitHub and Zenodo:- https://github.com/Shu12q/Raw-data.git.- Shu12q. (2023). Shu12q/Raw-data: First release of my data (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.8374644.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38274323", "locator": "sections[28] \"Additional Information and Declarations\" paragraph 4", "quote": "The following information was supplied regarding data availability:The data is available at NCBI GEO: GSE167297, GSE26901, GSE15459and the raw measurements are available at GitHub and Zenodo:- https://github.com/Shu12q/Raw-data.git.- Shu12q. (2023). Shu12q/Raw-data: First release of my data (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.8374644."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Among 86 common genes, seven prognostic factors (RGS2, GNAI2, ANXA5, MARCKS, CD36, NRP1 and PDE4A) were identified and composed a RiskScore model.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38274323", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Among 86 common genes, seven prognostic factors (RGS2, GNAI2, ANXA5, MARCKS, CD36, NRP1 and PDE4A) were identified and composed a RiskScore model."}, {"asset": "source:pmid:38274323", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "A prognostic scoring system was constructed by identifying prognostic factors in STAD by Least absolute shrinkage and selection operator (LASSO) COX model."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Among 86 common genes, seven prognostic factors (RGS2, GNAI2, ANXA5, MARCKS, CD36, NRP1 and PDE4A) were identified and composed a RiskScore model.", "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:38274323"], "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:GSE15459"], "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:GSE15459"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38274323", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.16776", "sha256": "sha256:b0ff748002700f6f99f15ad67cd2a007b70799bc89d216fb01bddd833e6047d1", "bytes": 43673, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.16776", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10809984", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15459", "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=GSE15459", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15459", "version": null, "note": "The following information was supplied regarding data availability:The data is available at NCBI GEO: GSE167297, GSE26901, GSE15459and the raw measurements are available at GitHub and Zenodo:- https://github.com/Shu12q/Raw-data.git.- Shu12q. (2023). Shu12q/Raw-data: First release of my data (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.8374644.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:The data is available at NCBI GEO: GSE167297, GSE26901, GSE15459and the raw measurements are available at GitHub and Zenodo:- https://github.com/Shu12q/Raw-data.git.- Shu12q. (2023). Shu12q/Raw-data: First release of my data (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.8374644.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM387788", "GSM387789", "GSM387790", "GSM387791", "GSM387792", "GSM387793", "GSM387794", "GSM387795", "GSM387796", "GSM387797", "GSM387798", "GSM387799", "GSM387800", "GSM387801", "GSM387802", "GSM387803", "GSM387804", "GSM387805", "GSM387806", "GSM387807", "GSM387808", "GSM387809", "GSM387810", "GSM387811", "GSM387812", "GSM387813", "GSM387814", "GSM387815", "GSM387816", "GSM387817", "GSM387818", "GSM387819", "GSM387820", "GSM387821", "GSM387822", "GSM387823", "GSM387824", "GSM387825", "GSM387826", "GSM387827", "GSM387828", "GSM387829", "GSM387830", "GSM387831", "GSM387832", "GSM387833", "GSM387834", "GSM387835", "GSM387836", "GSM387837", "GSM387838", "GSM387839", "GSM387840", "GSM387841", "GSM387842", "GSM387843", "GSM387844", "GSM387845", "GSM387846", "GSM387847", "GSM387848", "GSM387849", "GSM387850", "GSM387851", "GSM387852", "GSM387853", "GSM387854", "GSM387855", "GSM387856", "GSM387857", "GSM387858", "GSM387859", "GSM387860", "GSM387861", "GSM387862", "GSM387863", "GSM387864", "GSM387865", "GSM387866", "GSM387867", "GSM387868", "GSM387869", "GSM387870", "GSM387871", "GSM387872", "GSM387873", "GSM387874", "GSM387875", "GSM387876", "GSM387877", "GSM387878", "GSM387879", "GSM387880", "GSM387881", "GSM387882", "GSM387883", "GSM387884", "GSM387885", "GSM387886", "GSM387887", "GSM387888", "GSM387889", "GSM387890", "GSM387891", "GSM387892", "GSM387893", "GSM387894", "GSM387895", "GSM387896", "GSM387897", "GSM387898", "GSM387899", "GSM387900", "GSM387901", "GSM387902", "GSM387903", "GSM387904", "GSM387905", "GSM387906", "GSM387907", "GSM387908", "GSM387909", "GSM387910", "GSM387911", "GSM387912", "GSM387913", "GSM387914", "GSM387915", "GSM387916", "GSM387917", "GSM387918", "GSM387919", "GSM387920", "GSM387921", "GSM387922", "GSM387923", "GSM387924", "GSM387925", "GSM387926", "GSM387927", "GSM387928", "GSM387929", "GSM387930", "GSM387931", "GSM387932", "GSM387933", "GSM387934", "GSM387935", "GSM387936", "GSM387937", "GSM387938", "GSM387939", "GSM387940", "GSM387941", "GSM387942", "GSM387943", "GSM387944", "GSM387945", "GSM387946", "GSM387947", "GSM387948", "GSM387949", "GSM387950", "GSM387951", "GSM387952", "GSM387953", "GSM387954", "GSM387955", "GSM387956", "GSM387957", "GSM387958", "GSM387959", "GSM387960", "GSM387961", "GSM387962", "GSM387963", "GSM387964", "GSM387965", "GSM387966", "GSM387967", "GSM387968", "GSM387969", "GSM387970", "GSM387971", "GSM387972", "GSM387973", "GSM387974", "GSM387975", "GSM387976", "GSM387977", "GSM387978", "GSM387979", "GSM387980", "GSM387981", "GSM387982", "GSM387983", "GSM387984", "GSM387985", "GSM387986", "GSM387987"], "sample_count": 200, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gastric Cancer Project '08 (Singapore Patient Cohort)", "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:GSE167297", "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=GSE167297", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE167297", "version": null, "note": "The following information was supplied regarding data availability:The data is available at NCBI GEO: GSE167297, GSE26901, GSE15459and the raw measurements are available at GitHub and Zenodo:- https://github.com/Shu12q/Raw-data.git.- Shu12q. (2023). Shu12q/Raw-data: First release of my data (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.8374644.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:The data is available at NCBI GEO: GSE167297, GSE26901, GSE15459and the raw measurements are available at GitHub and Zenodo:- https://github.com/Shu12q/Raw-data.git.- Shu12q. (2023). Shu12q/Raw-data: First release of my data (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.8374644.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM5101013", "GSM5101014", "GSM5101015", "GSM5101016", "GSM5101017", "GSM5101018", "GSM5101019", "GSM5101020", "GSM5101021", "GSM5101022", "GSM5101023", "GSM5101024", "GSM5101025", "GSM5101026"], "sample_count": 14, "group_sizes": null, "group_sizes_basis": null, "platform": "20301", "taxon": "Homo sapiens", "title": "Spatially distinct reprogramming of the tumor microenvironment based on tumor invasion in diffuse-type gastric cancers", "resolution_checked_at": "2026-11-01T19:09:46Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE26901", "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=GSE26901", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26901", "version": null, "note": "The following information was supplied regarding data availability:The data is available at NCBI GEO: GSE167297, GSE26901, GSE15459and the raw measurements are available at GitHub and Zenodo:- https://github.com/Shu12q/Raw-data.git.- Shu12q. (2023). Shu12q/Raw-data: First release of my data (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.8374644.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:The data is available at NCBI GEO: GSE167297, GSE26901, GSE15459and the raw measurements are available at GitHub and Zenodo:- https://github.com/Shu12q/Raw-data.git.- Shu12q. (2023). Shu12q/Raw-data: First release of my data (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.8374644.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM662509", "GSM662510", "GSM662511", "GSM662512", "GSM662513", "GSM662514", "GSM662515", "GSM662516", "GSM662517", "GSM662518", "GSM662519", "GSM662520", "GSM662521", "GSM662522", "GSM662523", "GSM662524", "GSM662525", "GSM662526", "GSM662527", "GSM662528", "GSM662529", "GSM662530", "GSM662531", "GSM662532", "GSM662533", "GSM662534", "GSM662535", "GSM662536", "GSM662537", "GSM662538", "GSM662539", "GSM662540", "GSM662541", "GSM662542", "GSM662543", "GSM662544", "GSM662545", "GSM662546", "GSM662547", "GSM662548", "GSM662549", "GSM662550", "GSM662551", "GSM662552", "GSM662553", "GSM662554", "GSM662555", "GSM662556", "GSM662557", "GSM662558", "GSM662559", "GSM662560", "GSM662561", "GSM662562", "GSM662563", "GSM662564", "GSM662565", "GSM662566", "GSM662567", "GSM662568", "GSM662569", "GSM662570", "GSM662571", "GSM662572", "GSM662573", "GSM662574", "GSM662575", "GSM662576", "GSM662577", "GSM662578", "GSM662579", "GSM662580", "GSM662581", "GSM662582", "GSM662583", "GSM662584", "GSM662585", "GSM662586", "GSM662587", "GSM662588", "GSM662589", "GSM662590", "GSM662591", "GSM662592", "GSM662593", "GSM662594", "GSM662595", "GSM662596", "GSM662597", "GSM662598", "GSM662599", "GSM662600", "GSM662601", "GSM662602", "GSM662603", "GSM662604", "GSM662605", "GSM662606", "GSM662607", "GSM662608", "GSM662609", "GSM662610", "GSM662611", "GSM662612", "GSM662613", "GSM662614", "GSM662615", "GSM662616", "GSM662617"], "sample_count": 109, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Characterization of gene expression profiles of gastric cancer in Kosin University cohort", "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:GSE15459 not downloaded", "asset:data:geo:GSE15459 licence not read", "asset:data:geo:GSE167297 not downloaded", "asset:data:geo:GSE167297 licence not read", "asset:data:geo:GSE26901 not downloaded", "asset:data:geo:GSE26901 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 model was trained based on 5-fold cross-validation to select the penalty parameter λ."}}, {"id": "method-2", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}, {"id": "method-3", "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-4", "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": 0.8, "band": "high", "quote": "Log Rank"}}, {"id": "method-5", "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": 0.8, "band": "high", "quote": "limma"}}], "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": ["GSE167297", "GSE26901", "GSE15459"], "resolved_accessions": ["GSE167297", "GSE26901", "GSE15459"], "statements": ["The following information was supplied regarding data availability:The data is available at NCBI GEO: GSE167297, GSE26901, GSE15459and the raw measurements are available at GitHub and Zenodo:- https://github.com/Shu12q/Raw-data.git.- Shu12q. (2023). Shu12q/Raw-data: First release of my data (v1.0.0). Zenodo. https://doi.org/10.5281/zenodo.8374644."], "basis": "The paper names GSE167297, GSE26901, GSE15459 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:38274323", "data:geo:GSE15459"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE15459"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:06:42Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12329, "completion_tokens": 2859, "cached_tokens": 256}}, "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:38274323", "type": "paper", "label": "pmid:38274323"}, {"id": "source:pmid:38274323", "type": "manuscript", "label": "PMID 38274323 full text"}, {"id": "data:geo:GSE15459", "type": "dataset", "label": "GEO GSE15459"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38274323", "type": "paper", "label": "pmid:38274323"}, {"id": "source:pmid:38274323", "type": "manuscript", "label": "PMID 38274323 full text"}, {"id": "data:geo:GSE15459", "type": "dataset", "label": "GEO GSE15459"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38274323", "type": "extraction", "used": ["source:pmid:38274323"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE15459", "type": "accession_resolution", "used": ["data:geo:GSE15459"], "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:38274323", "parent_hash": "sha256:c5ccb8f9e5c38f208669cd5f5cbeb0bd7b90c498947bc6605be12db424e931ea", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE15459 licence not read", "asset:data:geo:GSE15459 not downloaded", "asset:data:geo:GSE167297 licence not read", "asset:data:geo:GSE167297 not downloaded", "asset:data:geo:GSE26901 licence not read", "asset:data:geo:GSE26901 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": "scrna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "unsupported", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["types. Methods: Single-cell sequencing data (scRNA-seq) GSE167297 and bulk RNA-seq data from TCGA,", "nscaling and annotating the cellular data in scRNA-seq, critical cell types in tumor progression we", "d by the CCK8 assay and cell cycle. Results: scRNA-seq analysis revealed that 11 cell types were id", "ata from STAD patients This study included a single-cell RNA sequencing project of STAD patients (registration numbe"], "order_basis": "paper_text_order:377", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["quencing data (scRNA-seq) GSE167297 and bulk RNA-seq data from TCGA, GTEx, GSE26901 and GSE15459", "459 datasets, and 359 normal stomach tissues transcriptome sequencing data from The Genotype-Tissue Exp", "N7 and MKN28 was consistent with that in the RNA-seq data in addition to comparison of protein ex", "of qRT-PCR matched the expression levels in RNA-seq data analysis. WB was conducted to detect th"], "order_basis": "paper_text_order:407", "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": 0.99, "evidence": ["of gastric cancer cells were examined by the CCK8 assay and cell cycle. Results: scRNA-seq ana", "observed by cell cycle (Figs. 7I and 7J) and CCK8 assays (Figs. 7K and 7L). Experimental valid", "MARCK5 expression. (K and L) Representative CCK8 results following inhibition of MARCK5 expre"], "order_basis": "paper_text_order:1518", "id": "assay:3"}, {"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 model was trained based on 5-fold cross-validation to select the penalty parameter λ."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}