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pmid:30026832
Distinct Diagnostic and Prognostic Values of Minichromosome Maintenance Gene Expression in Patients with Hepatocellular Carcinoma.
Xiwen Liao · Xiaoguang Liu · Chengkun Yang · Xiangkun Wang · Tingdong Yu · Chuangye Han · Ketuan Huang · Guangzhi Zhu · Hao Su · Wei Qin · Rui Huang · Long Yu · Jianlong Deng · Xianmin Zeng · Xinping Ye · Tao Peng
Journal of Cancer · 2018 doi:10.7150/jca.25221
Paper
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Experiment
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Data
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Complete file
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Methods: The biological function of the MCM genes were investigated by bioinformatics analysis. The diagnostic and prognostic values of the MCM genes were investigated by using the data of HCC patients from the GSE14520 and The Cancer Genome Atlas (TCGA) databases. Results: Bioinformatics analysis of the MCM genes substantiated that MCM2-7 genes were significantly enriched in DNA replication and cell cycle, and co-expressed with each other. These genes also co-expressed in HCC tumor tissue in both the GSE14520 and TCGA cohort. We also observed that the expression of the MCM2-7 genes was increased in tumor tissue, and diagnostic receiver operating characteristic analysis of MCM2-7 indicated that these genes could serve as sensitive diagnostic markers in HCC. Survival analysis in the GSE14520 cohort suggested that expression of MCM2, MCM4, MCM5, and MCM6 were significantly associated with hepatitis B virus-related HCC overall survival (OS). However, none of the MCM genes were associated with recurrence-free survival in the GSE14520 cohort. The validation cohort of TCGA suggested that the expression of MCM2, MCM6, and MCM7 were significantly correlated with HCC OS. Conclusion: Our study indicated that MCM2-7 genes may be potential diagnostic biomarkers in patients with HCC. Among them, MCM2 and MCM6 may serve as potential prognostic biomarkers for HCC.", "claims": [{"id": "claim-method", "statement": "Diagnostic values of the MCM genes in distinguishing HCC tumors from adjacent normal liver tissue were performed using the receiver operating characteristic (ROC) curve calculated using SPSS software.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30026832", "locator": "sections[5] \"Association analysis and diagnostic value assessment\" paragraph 2", "quote": "Diagnostic values of the MCM genes in distinguishing HCC tumors from adjacent normal liver tissue were performed using the receiver operating characteristic (ROC) curve calculated using SPSS software."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE14520 dataset of MCM gene expression and corresponding clinical data of hepatitis B virus (HBV)-related HCC were downloaded from the Gene Expression Omnibus database (https://www.ncbi. nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520, accessed December 15, 2017) 21, 22.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30026832", "locator": "sections[4] \"Data source\" paragraph 2", "quote": "The GSE14520 dataset of MCM gene expression and corresponding clinical data of hepatitis B virus (HBV)-related HCC were downloaded from the Gene Expression Omnibus database (https://www.ncbi. nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520, accessed December 15, 2017) 21, 22."}], "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:30026832"], "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": {"hazard_ratio": "whereas, hazard ratios (HRs) and 95% confidence in"}, "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:30026832", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/jca.25221", "sha256": "sha256:513adc256a3c62193c6d504b09559e98b4ceb96862ad991d3a2555c3a974da7e", "bytes": 56582, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7150/jca.25221", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6036720", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14520", "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=GSE14520", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14520", "version": null, "note": "The GSE14520 dataset of MCM gene expression and corresponding clinical data of hepatitis B 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"RFS", "", "OS"], ["NO. of event", "MRT (months)", "Crude HR (95% CI)", "Crude P", "Adjusted HR (95% CI)", "Adjusted P §", "", "NO. of event", "MST (months)", "Crude HR (95% CI)", "Crude P", "Adjusted HR (95% CI)", "Adjusted P §"], ["MCM2", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], ["Low", "106", "57", "51", "1", "", "1", "", "", "34", "NA", "1", "", "1", ""], ["High", "106", "59", "30", "1.200(0.834-1.728)", "0.326", "1.125(0.776-1.629)", "0.534", "", "48", "NA", "1.693(1.090-2.629)", "0.019", "1.587(1.016-2.480)", "0.043"], ["MCM3", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], ["Low", "106", "56", "48", "1", "", "1", "", "", "36", "NA", "1", "", "1", ""], ["High", "106", "60", "36", "1.268(0.880-1.826)", "0.202", "1.306(0.905-1.885)", "0.154", "", "46", "NA", "1.502(0.971-2.324)", "0.068", "1.516(0.976-2.354)", "0.064"], ["MCM4", "", "", "", "", "", "", "", "", "", "", "", "", "", ""], ["Low", "106", "56", "51", "1", "", "1", "", "", "35", "NA", "1", "", 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{"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"}}, {"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's correlation"}}, {"id": "method-4", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "protein-protein interaction"}}, {"id": "method-5", "family": null, "specific": null, "label": "Receiver operating characteristic (ROC) curve analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Diagnostic values of the MCM genes in distinguishing HCC tumors from adjacent normal liver tissue were performed using the receiver operating characteristic (ROC) curve calculated using SPSS software."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["GSE14520"], "resolved_accessions": ["GSE14520"], "statements": ["The GSE14520 dataset of MCM gene expression and corresponding clinical data of hepatitis B virus (HBV)-related HCC were downloaded from the Gene Expression Omnibus database (https://www.ncbi. nlm.nih.gov/geo/query/acc.cgi?acc=GSE14520, accessed December 15, 2017) 21, 22."], "basis": "The paper names GSE14520 in Gene Expression Omnibus and the accession resolves in the repository. 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