Early B-cell factors involve in the tumorigenesis and predict the overall survival of gastric cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34100918", "kind": "science-record", "revision": 7, "content_hash": "sha256:38cf20976cbb7b3690ca33d2920108e9a314cfcebab43d971ccd569aea0eb97a", "created_at": "2026-11-01T15:41:38Z", "updated_at": "2026-11-01T22:03:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Early B-cell factors involve in the tumorigenesis and predict the overall survival of gastric cancer.", "doi": "10.1042/BSR20210055", "pmid": "34100918", "authors": ["Qing Wang", "Jiahong Liang", "Xianyu Hu", "Songgang Gu", "Qiaodong Xu", "Jiang Yan"], "journal": "Bioscience reports", "year": 2021, "abstract": "Gastric cancer (GC) is a heavy health burden around the world, which is the fifth most frequent tumor and leads to the third most common cancer-related deaths. It is urgent to identify prognostic markers as the guideline for personalized treatment and follow-up. We accessed the prognostic value of Early B-cell factors (EBFs) in GC. A total of 415 GC tissues and 34 normal tissues from The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD) cohort, 616 external patients from GSE15459, GSE22377, GSE51105, GSE62245 were enrolled for analysis. Univariate and multivariate Cox regression analyses were employed to evaluate the sole and integrative prognostic value of EBFs, respectively. Genetic alterations, DNA methylation of EBFs were also evaluated, as well as the involved signaling pathways. We revealed that increased EBFs associated with the poor prognosis of GC patients, the prognostic model was established in TCGA-STAD cohort, and validated in Gene Expression Omnibus (GEO) cohorts, with effectiveness in both HER2 positive and negative patients. DNA methylation was involved in the impact on prognosis. Cell cycle, immune-associated, and MAPK pathways were influenced by EBFs. Anti-CTLA4 immunotherapy is more suitable for EBFs determining high-risk groups, but not anti-PD-1/PD-L1 therapy. 5-Fluorouracil, methotrexate, vorinostat are suitable to inhibit the function of EBFs. Our new findings provide novel insight into the prediction of prognosis and clinical treatment of GC patients based on EBFs.", "claims": [{"id": "claim-method", "statement": "K–M survival analysis was used to indicate the different clinical outcomes of subgroups. A total of 415 GC tissues and 34 normal tissues from The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD) cohort was enrolled from The Cancer Genome Atlas (TCGA) project (https://www.cancer.gov), data of transcription profiling (mRNA SeqV2), genetic alterations (gene level) and methylation (Methylation450k) for EBFs were all obtained from TCGA project. Furthermore, another 616 GC patients were also enrolled from Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/), GSE15459 (n=197), GSE22377 (n=43), GSE51105 (n=93), and GSE62245 (n=283).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34100918", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "K–M survival analysis was used to indicate the different clinical outcomes of subgroups."}, {"asset": "source:pmid:34100918", "locator": "sections[3] \"Collection of GC patient cohorts\" paragraph 2", "quote": "A total of 415 GC tissues and 34 normal tissues from The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD) cohort was enrolled from The Cancer Genome Atlas (TCGA) project (https://www.cancer.gov), data of transcription profiling (mRNA SeqV2), genetic alterations (gene level) and methylation (Methylation450k) for EBFs were all obtained from TCGA project."}, {"asset": "source:pmid:34100918", "locator": "sections[3] \"Collection of GC patient cohorts\" paragraph 2", "quote": "Furthermore, another 616 GC patients were also enrolled from Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/), GSE15459 (n=197), GSE22377 (n=43), GSE51105 (n=93), and GSE62245 (n=283)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of the present study are included within the article. The gene expression data can be accessed on TCGA and GEO.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34100918", "locator": "sections[25] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of the present study are included within the article. The gene expression data can be accessed on TCGA and GEO."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": null, "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:34100918"], "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": "blocked", "blocked_on": "method:group_comparison_wilcoxon", "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": ["step:run_analysis blocked on method:group_comparison_wilcoxon"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34100918", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1042/BSR20210055", "sha256": "sha256:1f324a26715571208d8349b8f4f892628b8069b8718cd12cd0abd5eb3b59a52a", "bytes": 32628, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1042/BSR20210055", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8239495", "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 data used to support the findings of the present study are included within the article. 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"available", "identifier": "section[21]/table-wrap[1]#T3", "version": null, "note": "Prediction of the potential treatment small molecules of EBFs", "structure": {"pmcid": "PMC8239495", "section_index": 21, "section_title": "Anti-CTLA4 and several small molecules are effective treatments for EBF-determined high-risk group", "row_count": 64, "column_count": 4}, "table": {"label": "Table 3", "caption": "Prediction of the potential treatment small molecules of EBFs", "rows": [["Gene symbol", "Drug name", "Correlation", "FDR"], ["EBF1", "5-Fluorouracil", "−0.18", "<0.01"], ["EBF2", "5-Fluorouracil", "−0.1", "<0.01"], ["EBF3", "5-Fluorouracil", "−0.13", "<0.01"], ["EBF1", "AR-42", "−0.24", "<0.01"], ["EBF2", "AR-42", "−0.14", "<0.01"], ["EBF3", "AR-42", "−0.14", "<0.01"], ["EBF1", "AT-7519", "−0.21", "<0.01"], ["EBF2", "AT-7519", "−0.14", "<0.01"], ["EBF3", "AT-7519", "−0.12", "<0.01"], ["EBF1", "CAY10603", "−0.28", "<0.01"], ["EBF2", "CAY10603", "−0.14", "<0.01"], ["EBF3", "CAY10603", 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"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": 0.7, "band": "medium", "quote": "Cox regression"}}, {"id": "method-3", "family": "correlation_analysis", "specific": "pearson", "label": "Correlation analysis", "dsl_operations": ["pearson_r"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["paired_numeric_columns"], "evidence": {"score": 0.8, "band": "high", "quote": "Pearson correlation"}}, {"id": "method-4", "family": null, "specific": null, "label": "K–M survival analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "reordered", "quote": "K–M survival analysis was used to indicate the different clinical outcomes of subgroups. A total of 415 GC tissues and 34 normal tissues from The Cancer Genome Atlas Stomach Adenocarcinoma (TCGA-STAD) cohort was enrolled from The Cancer Genome Atlas (TCGA) project (https://www.cancer.gov), data of transcription profiling (mRNA SeqV2), genetic alterations (gene level) and methylation (Methylation450k) for EBFs were all obtained from TCGA project. Furthermore, another 616 GC patients were also enrolled from Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/), GSE15459 (n=197), GSE22377 (n=43), GSE51105 (n=93), and GSE62245 (n=283)."}}], "targets": [], "gaps": ["method.reader_named_unmapped", "method.group_comparison_wilcoxon"]}, "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": ["group_comparison_wilcoxon"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: wilcoxon."}, "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": ["GSE15459", "GSE22377", "GSE51105", "GSE62245"], "resolved_accessions": ["GSE15459", "GSE22377", "GSE51105", "GSE62245"], "statements": ["The data used to support the findings of the present study are included within the article. The gene expression data can be accessed on TCGA and GEO."], "basis": "The paper names GSE15459, GSE22377, GSE51105, GSE62245 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": [], "assets": ["source:pmid:34100918", "data:geo:GSE15459", "asset:table:pmid:34100918:1", "asset:table:pmid:34100918:2", "asset:table:pmid:34100918:3"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "group_comparison_wilcoxon", "unlocks_papers": null, "priority": null}], "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": "2026-10-31T18:30:51Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 25880, "completion_tokens": 3638, "cached_tokens": 784}}, "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:34100918", "type": "paper", "label": "pmid:34100918"}, {"id": "source:pmid:34100918", "type": "manuscript", "label": "PMID 34100918 full text"}, {"id": "data:geo:GSE15459", "type": "dataset", "label": "GEO GSE15459"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34100918", "type": "paper", "label": "pmid:34100918"}, {"id": "source:pmid:34100918", "type": "manuscript", "label": "PMID 34100918 full text"}, {"id": "data:geo:GSE15459", "type": "dataset", "label": "GEO GSE15459"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34100918", "type": "extraction", "used": ["source:pmid:34100918"], "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:34100918", "parent_hash": "sha256:b573a68b7ac8f73ec0aa5d09bbb3e9593aa449af0f6df92ddb66cb73b4d51a53", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE15459 licence not read", "asset:data:geo:GSE15459 not downloaded", "asset:data:geo:GSE22377 licence not read", "asset:data:geo:GSE22377 not downloaded", "asset:data:geo:GSE51105 licence not read", "asset:data:geo:GSE51105 not downloaded", "asset:data:geo:GSE62245 licence not read", "asset:data:geo:GSE62245 not downloaded", "execution.not_run", "method.group_comparison_wilcoxon", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:group_comparison_wilcoxon"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["lection (ATCC, Manassas, VA), and cells were cultured in RPMI-1640 medium with 10% fetal bovine serum"], "order_basis": "paper_text_order:2699", "id": "assay:1"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["Wilcoxon"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}