UBE2C Is a Potential Biomarker of Intestinal-Type Gastric Cancer With Chromosomal Instability.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30116193", "kind": "science-record", "revision": 8, "content_hash": "sha256:9111e14f2e42e777328f1339646349a93296d01d3986fdc41564fc74ff8f207c", "created_at": "2026-11-01T15:40:36Z", "updated_at": "2026-11-01T22:00:00Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "UBE2C Is a Potential Biomarker of Intestinal-Type Gastric Cancer With Chromosomal Instability.", "doi": "10.3389/fphar.2018.00847", "pmid": "30116193", "authors": ["Jun Zhang", "Xinyu Liu", "Guanzhen Yu", "Lei Liu", "Jiejun Wang", "Xiaoyu Chen", "Yuhai Bian", "Yuan Ji", "Xiaoyan Zhou", "Yinan Chen", "Jun Ji", "Zhen Xiang", "Lei Guo", "Jingyuan Fang", "Yihong Sun", "Hui Cao", "Zhenggang Zhu", "Yingyan Yu"], "journal": "Frontiers in pharmacology", "year": 2018, "abstract": "This study explored potential biomarkers associated with Lauren classification of gastric cancer. We screened microarray datasets on gastric cancer with information of Lauren classification in gene expression omnibus (GEO) database, and compared differentially expressing genes between intestinal-type or diffuse-type gastric cancer. Four sets of microarray data (GSE2669, GSE2680, GDS3438, and GDS4007) were enrolled into analysis. By differential gene analysis, UBE2C, CDH1, CENPF, ERO1L, SCD, SOX9, CKS1B, SPP1, MMP11, and ANLN were identified as the top genes related to intestinal-type gastric cancer, and MGP, FXYD1, FAT4, SIPA1L2, MUC5AC, MMP15, RAB23, FBLN1, ANXA10, and ADH1B were genes related to diffuse-type gastric cancer. We comprehensively validated the biological functions of the intestinal-type gastric cancer related gene UBE2C and evaluated its clinical significance on 1,868 cases of gastric cancer tissues from multiple medical centers of Shanghai, China. The gain of copy number on 20q was found in 4 out of 5 intestinal-type cancer cell lines, and no similar copy number variation (CNV) was found in any diffuse-type cancer cell line. Interfering UBE2C expression inhibited cell proliferation, migration and invasion in vitro, and tumorigenesis in vivo. Knockdown of UBE2C resulted in G2/M blockage in intestinal-type gastric cancer cells. Overexpression of UBE2C activated ERK signal pathway and promoted cancer cell proliferation. U0126, an inhibitor of ERK signaling pathway reversed the oncogenic phenotypes caused by UBE2C. Moreover, overexpression of UBE2C was identified in human intestinal-type gastric cancer. Overexpression of UBE2C protein predicted poor clinical outcome. Taken together, we characterized a group of Lauren classification-associated biomarkers, and clarified biological functions of UBE2C, an intestinal-type gastric cancer associated gene. Overexpression of UBE2C resulted in chromosomal instability that disturbed cell cycle and led to poor prognosis of intestinal-type gastric cancer.", "claims": [{"id": "claim-data-access", "statement": "We searched gene expression omnibus (GEO) database of NCBI (http://www.ncbi.nlm.nih.gov/geo/) using keywords of “Gastric Cancer,” “Gastric Carcinoma” or “Stomach cancer,” and obtained four sets of microarray datasets (GEO serial numbers: GSE2669, GSE2680, GSE3438, and GSE4007) that included detail information of Lauren classification.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30116193", "locator": "sections[3] \"DNA microarray data analysis\" paragraph 2", "quote": "We searched gene expression omnibus (GEO) database of NCBI (http://www.ncbi.nlm.nih.gov/geo/) using keywords of “Gastric Cancer,” “Gastric Carcinoma” or “Stomach cancer,” and obtained four sets of microarray datasets (GEO serial numbers: GSE2669, GSE2680, GSE3438, and GSE4007) that included detail information of Lauren classification."}], "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:30116193"], "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:GSE2669"], "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:student_t", "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:GSE2669"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30116193", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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"We searched gene expression omnibus (GEO) database of NCBI (http://www.ncbi.nlm.nih.gov/geo/) using keywords of “Gastric Cancer,” “Gastric Carcinoma” or “Stomach cancer,” and obtained four sets of microarray datasets (GEO serial numbers: GSE2669, GSE2680, GSE3438, and GSE4007) that included detail information of Lauren classification.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We searched gene expression omnibus (GEO) database of NCBI (http://www.ncbi.nlm.nih.gov/geo/) using keywords of “Gastric Cancer,” “Gastric Carcinoma” or “Stomach cancer,” and obtained four sets of microarray datasets (GEO serial numbers: GSE2669, GSE2680, GSE3438, and GSE4007) that included detail information of Lauren classification.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM51810", "GSM51811", "GSM51812", "GSM51813", "GSM51814", "GSM51815", "GSM51816", "GSM51817", "GSM51818", "GSM51819", "GSM51820", 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"124", "64 cancer26 gastritis22 metaplasia10 normal2 other", "Boussioutas A, National Cancer Centre of Singapore"], ["GSE2680", "Mixture of normal samples", "90", "68 intestinal-13 diffuse-9 mixed-", "Aggarwa A, National Cancer Centre of Singapore"], ["GSE3438", "Exchange of marked staining reagents", "100", "50 cancer50 normal", "Kim S, Korea Research Institute of Bioscience and Biotechnology"], ["GSE4007", "Mixture of normal samples", "126", "90 cancer22 normal14 lymph node", "Chen X, Stanford University"]], "row_count": 5, "column_count": 5, "numeric_cells": 12, "header_rows": 1, "locator": "section[15]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:30116193:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:93cbff4976b608f2652f9f2bef57a101c07c775d44eb1ca397538745fe98fe9a", "bytes": 1485, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[15]/table-wrap[2]#T2", "version": null, "note": "The top 10 related genes in intestinal- or diffuse-type gastric cancer.", "structure": {"pmcid": "PMC6082955", "section_index": 15, "section_title": "Data mining revealed genes related to lauren classification", "row_count": 23, "column_count": 3}, "table": {"label": "Table 2", "caption": "The top 10 related genes in intestinal- or diffuse-type gastric cancer.", "rows": [["Gene symbol", "Gene names", "Chromosome loci"], ["INTESTINAL-TYPE"], ["UBE2C", "Ubiquitin-conjugating enzyme E2C", "20q13.12"], ["CDH1", "Cadherin 1, type 1, E-cadherin (epithelial)", "16q22.1"], ["ERO1L", "ERO1-like (S. cerevisiae)", "14q22.1"], ["SCD", "Stearoyl-CoA desaturase (delta-9-desaturase)", "10q24.31"], ["SOX9", "SRY (sex determining region Y)-box 9", "17q24.3-q25.1"], ["CKS1B", "CDC28 protein kinase regulatory subunit 1Apseudogene", "8q21.13"], ["SPP1", "Osteopontin", "4q21-q25"], ["MMP11", "Matrix metallopeptidase 11 (stromelysin 3)", "22q11.2|22q11.23"], ["CENPF", "Centromere protein F, 350/400 ka (mitosin)", "1q32-q41"], ["ANLN", "Anillin, actin binding protein", "7p15-p14"], ["DIFFUSE-TYPE"], ["FAT4", "FAT tumor suppressor homolog 4 (Drosophila)", "4q28.1"], ["SIPA1L2", "Signal-induced proliferation-associated 1 like 2", "1q42.2"], ["RAB23", "RAB23, member RAS oncogene family", "6p11"], ["FBLN1", "Fibulin 1", "22q13.31"], ["ADH1B", "Alcohol dehydrogenase 1B (class I), beta polypeptide", "4q21-q23"], ["ANXA10", "Annexin A10", "4q33"], ["MGP", "Matrix Gla protein", "12p13.1-p12.3"], ["MUC5AC", "Mucin 5AC, oligomeric mucus/gel-forming", "11p15.5"], ["FXYD1", "FXYD domain containing ion transport regulator 1", "19q13.1"], ["MMP15", "Matrix metallopeptidase 15 (membrane-inserted)", "16q13-q21"]], "row_count": 23, "column_count": 3, "numeric_cells": 39, "header_rows": 1, "locator": "section[15]/table-wrap[2]#T2"}}], "gaps": ["asset:data:geo:GSE2669 not downloaded", "asset:data:geo:GSE2669 licence not read", 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"axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["student_t"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: student_t_test."}, "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": ["GSE2669", "GSE2680", "GSE3438", "GSE4007"], "resolved_accessions": ["GSE2669", "GSE2680", "GSE3438", "GSE4007"], "statements": ["We searched gene expression omnibus (GEO) database of NCBI (http://www.ncbi.nlm.nih.gov/geo/) using keywords of “Gastric Cancer,” “Gastric Carcinoma” or “Stomach cancer,” and obtained four sets of microarray datasets (GEO serial numbers: GSE2669, GSE2680, GSE3438, and GSE4007) that included detail information of Lauren classification."], "basis": "The paper names GSE2669, GSE2680, GSE3438, GSE4007 in Gene Expression Omnibus (GEO) database of NCBI and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:30116193", "data:geo:GSE2669", "asset:table:pmid:30116193:1", "asset:table:pmid:30116193:2"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "student_t", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE2669"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:35:42Z", "independence": "single_reader"}, "evidence_check": {"method": "absent", "availability": null}, "calls": 3, "usage": {"prompt_tokens": 30595, "completion_tokens": 1869, "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:30116193", "type": "paper", "label": "pmid:30116193"}, {"id": "source:pmid:30116193", "type": "manuscript", "label": "PMID 30116193 full text"}, {"id": "data:geo:GSE2669", "type": "dataset", "label": "GEO GSE2669"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:30116193", "type": "paper", "label": "pmid:30116193"}, {"id": "source:pmid:30116193", "type": "manuscript", "label": "PMID 30116193 full text"}, {"id": "data:geo:GSE2669", "type": "dataset", "label": "GEO GSE2669"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-30116193", "type": "extraction", "used": ["source:pmid:30116193"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE2669", "type": "accession_resolution", "used": ["data:geo:GSE2669"], "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:30116193", "parent_hash": "sha256:4bd941a9c3b6535d3a60c3fe88c23035240047029514f09eae46f51cac81b527", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE2669 licence not read", "asset:data:geo:GSE2669 not downloaded", "asset:data:geo:GSE2680 licence not read", "asset:data:geo:GSE2680 not downloaded", "asset:data:geo:GSE3438 licence not read", "asset:data:geo:GSE3438 not downloaded", "asset:data:geo:GSE4007 licence not read", "asset:data:geo:GSE4007 not downloaded", "execution.not_run", "method.student_t", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:student_t"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["lassification of gastric cancer. We screened microarray datasets on gastric cancer with information", "or diffuse-type gastric cancer. Four sets of microarray data (GSE2669, GSE2680, GDS3438, and GDS4007", "BGC-823, MKN-45, MKN-28, AGS, and HTB-103 by Affymetrix® Genome-Wide Human SNP Array 6.0 chip. The p"], "order_basis": "paper_text_order:160", "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": 0.77, "evidence": ["ion and invasion in vitro, and tumorigenesis in vivo. 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Statistical analysis Statistical analysis w"], "order_basis": "paper_text_order:1328", "id": "assay:3"}, {"role": "data_generation", "definition_id": "clinical_cohort", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["ide Human SNP Array 6.0 chip. 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