Identification of the potential therapeutic target gene UBE2C in human hepatocellular carcinoma: An investigation based on GEO and TCGA databases.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31186759", "kind": "science-record", "revision": 6, "content_hash": "sha256:86245cdb9f6b630b55c3e77e60ee8495714d40548b3e4ccc0dafa8f275573a49", "created_at": "2026-11-01T15:40:45Z", "updated_at": "2026-11-01T21:22:14Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the potential therapeutic target gene UBE2C in human hepatocellular carcinoma: An investigation based on GEO and TCGA databases.", "doi": "10.3892/ol.2019.10232", "pmid": "31186759", "authors": ["Zilun Wei", "Yihai Liu", "Shuaihua Qiao", "Xueling Li", "Qiaoling Li", "Jinxuan Zhao", "Jiaxin Hu", "Zhonghai Wei", "Anqi Shan", "Xuan Sun", "Biao Xu"], "journal": "Oncology letters", "year": 2019, "abstract": "Hepatocellular carcinoma (HCC) ranks the third major cause of cancer-associated mortality globally. Numerous studies have attempted to elucidate the underlying mechanisms of HCC using various biomarkers. In the present study, two expression profiles datasets from Gene Expression Omnibus (GSE76427 and GSE84402) and data associated with liver cancer samples from The Cancer Genome Atlas (TCGA) were downloaded for integrated analysis. Five differentially expressed genes (DEGs) exhibiting high expression, including ubiquitin-conjugating enzyme 2C (UBE2C), topoisomerase II α, pituitary tumor transforming gene 1, glypican-3 and polycomb-repressive complex 1, were selected and considered as candidate genes. Enrichment analysis demonstrated that these genes were associated with Gene Ontology terms of cellular components and molecular functions, including regulation of apoptosis, stabilization of p53 and Anaphase Promoting Complex/Cyclosome (APC/C) (APC/C:Cdc20)-mediated degradation of Securin. The expression profiles of these genes in HCC, other human malignancies and different human HCC cell lines were validated using GSE14520, GSE3500 and TCGA data. The results confirmed the upregulation of UBE2C in tissues from patients with HCC or other human malignancies and human liver cancer cell lines, compared with the expression levels in the corresponding adjacent non-tumor tissues and cell lines, respectively. Patients with HCC who exhibited an increased messenger RNA level of UBE2C exhibited a significantly shorter survival time. The results of the present study suggest that the overexpression of UBE2C may be used as a novel prognostic biomarker of HCC.", "claims": [{"id": "claim-method", "statement": "Survival analysis of patients with high expression of candidate DEGs in TCGA HCC data was performed using Kaplan-Meier estimator survival curves with several clinicopathological characteristics taken into consideration, including sex and pathological stage. Data was obtained from cBioPortal (http://www.cbioportal.org) and Kaplan-Meier Plotter (http://kmplot.com/analysis/) was used for analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31186759", "locator": "sections[9] \"Survival association of candidate genes with clinicopathological parameters of patients with HCC\" paragraph 2", "quote": "Survival analysis of patients with high expression of candidate DEGs in TCGA HCC data was performed using Kaplan-Meier estimator survival curves with several clinicopathological characteristics taken into consideration, including sex and pathological stage. Data was obtained from cBioPortal (http://www.cbioportal.org) and Kaplan-Meier Plotter (http://kmplot.com/analysis/) was used for analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed in the present study are all available on NCBI GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31186759", "locator": "sections[20] \"Availability of data and materials\" paragraph 2", "quote": "The datasets analyzed in the present study are all available on NCBI GEO (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "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:31186759"], "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:GSE14520"], "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:GSE14520"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31186759", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/ol.2019.10232", "sha256": 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"access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2233086", "GSM2233087", "GSM2233088", "GSM2233089", "GSM2233090", "GSM2233091", "GSM2233092", "GSM2233093", "GSM2233094", "GSM2233095", "GSM2233096", "GSM2233097", "GSM2233098", "GSM2233099", "GSM2233100", "GSM2233101", "GSM2233102", "GSM2233103", "GSM2233104", "GSM2233105", "GSM2233106", "GSM2233107", "GSM2233108", "GSM2233109", "GSM2233110", "GSM2233111", "GSM2233112", "GSM2233113"], "sample_count": 28, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from human hepatocellular carcinoma tissues and the correponding non-cancerous tissues", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:31186759:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", 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"asset:data:geo:GSE3500 not downloaded", "asset:data:geo:GSE3500 licence not read", "asset:data:geo:GSE76427 not downloaded", "asset:data:geo:GSE76427 licence not read", "asset:data:geo:GSE84402 not downloaded", "asset:data:geo:GSE84402 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": "Survival analysis of patients with high expression of candidate DEGs in TCGA HCC data was performed using Kaplan-Meier estimator survival curves with several clinicopathological characteristics taken into consideration, including sex and pathological stage. Data was obtained from cBioPortal (http://www.cbioportal.org) and Kaplan-Meier Plotter (http://kmplot.com/analysis/) was used for analysis."}}, {"id": "method-2", "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"}}], "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. 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