Bioinformatics analyses for the identification of tumor antigens and immune subtypes of gastric adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36579327", "kind": "science-record", "revision": 2, "content_hash": "sha256:08cc71c7a6b98835c7b237a43dfa1036d4c9980014c75a00998ebf474d36b401", "created_at": "2026-11-01T19:01:08Z", "updated_at": "2026-11-01T21:29:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analyses for the identification of tumor antigens and immune subtypes of gastric adenocarcinoma.", "doi": "10.3389/fgene.2022.1068112", "pmid": "36579327", "authors": ["Shuxun Wei", "Qiang Sun", "Jinshui Chen", "Xinxing Li", "Zhiqian Hu"], "journal": "Frontiers in genetics", "year": 2022, "abstract": "Background: Although mRNA vaccines have been effective against multiple cancers, their efficacy against stomach adenocarcinoma (STAD) remains undefined. Immunotyping can indicate the comprehensive immune status in tumors and their immune microenvironment, which is closely associated with therapeutic response and vaccination potential. The aim of this study was to identify potential antigens in STAD for mRNA vaccine development, and further distinguish immune subtypes of STAD to construct an immune landscape for selecting suitable patients for vaccination. Methods: The gene expression and clinicopathological features of patients with gastric cancer were downloaded from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression Program (GTEx). 729 samples from GSE66229 and GSE84437 were downloaded through GEO and were used as the validation cohorts. Differential gene expression, genetic alterations and prognosis were analyzed using the R package, cBioPortal program and Kaplan-Meier. The relationship between tumor antigens and immune cells was evaluated and plotted by TIMER. ConsensusClusterPlus was used for consistency matrix construction and data clustering, and graph learning-based dimensional reduction was used to depict immune landscape. WGCNA was used to estimate the relationship between the color modules and immune subtypes. Results: Two overexpressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in STAD, including RAI14 and NREP. The immune subtypes showed distinct molecular, cellular and clinical characteristics. IS1 and IS2 exhibited immune-activated phenotypes and correlated to better survival compared to IS3, while IS3 tumors was immunologically cold. Immunogenic cell death modulators, immune checkpoints, and CA125, and CEA were also differentially expressed among the three immune subtypes. Finally, the immune landscape of STAD showed a high degree of heterogeneity between individual patients. Conclusion: RAI14 and NREP are potential antigens for developing anti-STAD mRNA vaccine, and patients with IS1 and IS3 tumors may be suitable for vaccination.", "claims": [{"id": "claim-method", "statement": "The differentially expressed genes (DEGs) between STAD and normal tissue were identified by the Wilcox test with the criteria of |log2FC| > 1 and p-value <0.01. Based on the cBioPortal for Cancer Genomics (cBioPortal, http://www.cbioportal.org), DEGs with significant genetic alterations (p-value <0.05) were further selected for survival analysis. Genes with p-value < 0.01 in Kaplan-Meier method of overall survival (OS) and recurrence-free survival (RFS) were taken for candidate tumor antigens.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36579327", "locator": "sections[5] \"Identification of tumor antigens\" paragraph 2", "quote": "The differentially expressed genes (DEGs) between STAD and normal tissue were identified by the Wilcox test with the criteria of |log2FC| > 1 and p-value <0.01. Based on the cBioPortal for Cancer Genomics (cBioPortal, http://www.cbioportal.org), DEGs with significant genetic alterations (p-value <0.05) were further selected for survival analysis. Genes with p-value < 0.01 in Kaplan-Meier method of overall survival (OS) and recurrence-free survival (RFS) were taken for candidate tumor antigens."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36579327", "locator": "sections[19] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Two overexpressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in STAD, including RAI14 and NREP.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36579327", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Two overexpressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in STAD, including RAI14 and NREP."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Two overexpressed and mutated tumor antigens associated with poor prognosis and infiltration of antigen presenting cells were identified in STAD, including RAI14 and NREP.", "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:36579327"], "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:GSE66229"], "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:GSE66229"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36579327", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2022.1068112", "sha256": "sha256:01a398ff1092c25d71c3353d3f79f98e65c41bef6e50ca3996a5779c252f48dd", "bytes": 33352, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3389/fgene.2022.1068112", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9791036", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE66229", "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=GSE66229", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE66229", "version": null, "note": "The datasets presented in this study can be found in online repositories. 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"sample_count": 483, "group_sizes": null, "group_sizes_basis": null, "platform": "6947", "taxon": "Homo sapiens", "title": "Molecular subtypes in gastric cancer.", "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:GSE66229 not downloaded", "asset:data:geo:GSE66229 licence not read", "asset:data:geo:GSE84437 not downloaded", "asset:data:geo:GSE84437 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "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": 1.0, "band": "verbatim", "quote": "The differentially expressed genes (DEGs) between STAD and normal tissue were identified by the Wilcox test with the criteria of |log2FC| > 1 and p-value <0.01. Based on the cBioPortal for Cancer Genomics (cBioPortal, http://www.cbioportal.org), DEGs with significant genetic alterations (p-value <0.05) were further selected for survival analysis. Genes with p-value < 0.01 in Kaplan-Meier method of overall survival (OS) and recurrence-free survival (RFS) were taken for candidate tumor antigens."}}], "targets": [], "gaps": []}, "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE66229", "GSE84437"], "resolved_accessions": ["GSE66229", "GSE84437"], "statements": ["The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."], "basis": "The paper names GSE66229, GSE84437 in GEO DataSets and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:36579327", "data:geo:GSE66229"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE66229"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:22:01Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9201, "completion_tokens": 2700, "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:36579327", "type": "paper", "label": "pmid:36579327"}, {"id": "source:pmid:36579327", "type": "manuscript", "label": "PMID 36579327 full text"}, {"id": "data:geo:GSE66229", "type": "dataset", "label": "GEO GSE66229"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36579327", "type": "paper", "label": "pmid:36579327"}, {"id": "source:pmid:36579327", "type": "manuscript", "label": "PMID 36579327 full text"}, {"id": "data:geo:GSE66229", "type": "dataset", "label": "GEO GSE66229"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36579327", "type": "extraction", "used": ["source:pmid:36579327"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE66229", "type": "accession_resolution", "used": ["data:geo:GSE66229"], "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:36579327", "parent_hash": "sha256:7d651fbb8f5c2e77256d44a725a4100cb8b5cb61ad6a578e501702b263599eba", "fork_of": null, "generation": 1}, "gaps": ["asset:data:geo:GSE66229 licence not read", "asset:data:geo:GSE66229 not downloaded", "asset:data:geo:GSE84437 licence not read", "asset:data:geo:GSE84437 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The differentially expressed genes (DEGs) between STAD and normal tissue were identified by the Wilcox test with the criteria of |log2FC| > 1 and p-value <0.01. Based on the cBioPortal for Cancer Genomics (cBioPortal, http://www.cbioportal.org), DEGs with significant genetic alterations (p-value <0.05) were further selected for survival analysis. Genes with p-value < 0.01 in Kaplan-Meier method of overall survival (OS) and recurrence-free survival (RFS) were taken for candidate tumor antigens."], "order_basis": "analysis_only", "id": "assay:1"}]}