Identification of a Five-Gene Signature for Predicting Survival in Malignant Pleural Mesothelioma Patients.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32849853", "kind": "science-record", "revision": 8, "content_hash": "sha256:5ba4a41a00d3627a9960ca3f564d4f78693967dc94ba1d6139c64d057ae69dfb", "created_at": "2026-11-01T15:41:08Z", "updated_at": "2026-11-01T22:45:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a Five-Gene Signature for Predicting Survival in Malignant Pleural Mesothelioma Patients.", "doi": "10.3389/fgene.2020.00899", "pmid": "32849853", "authors": ["Yiyang Bai", "Xiao Wang", "Jia Hou", "Luying Geng", "Xuan Liang", "Zhiping Ruan", "Hui Guo", "Kejun Nan", "Lili Jiang"], "journal": "Frontiers in genetics", "year": 2020, "abstract": "Malignant pleural mesothelioma (MPM), predominantly caused by asbestos exposure, is a highly aggressive cancer with poor prognosis. The staging systems currently used in clinics is inadequate in evaluating the prognosis of MPM. In this study, a five-gene signature was developed and enrolled into a prognostic risk score model by LASSO Cox regression analysis based on two expression profiling datasets (GSE2549 and GSE51024) from Gene Expression Omnibus (GEO). The five-gene signature was further validated using the Cancer Genome Atlas (TCGA) MPM dataset. Univariate and multivariate Cox analyses proved that the five-gene signature was an independent prognostic factor for MPM. The signature remained statistically significant upon stratification by Brigham stage, AJCC stage, gender, tumor size, and lymph node status. Time-dependent receiver operating characteristic (ROC) curve indicated good performance of our model in predicting 1- and 2-years overall survival in MPM patients. The C-index was 0.784 for GSE2549 and 0.753 for the TCGA dataset showing moderate predictive accuracy of our model. Furthermore, Gene Set Enrichment Analysis suggested that the five-gene signature was related to pathways resulting in MPM tumor progression. Together, we have established a five-gene signature significantly associated with prognosis in MPM patients. Hence, the five-genes signature may serve as a potentially useful prognostic tool for MPM patients.", "claims": [{"id": "claim-method", "statement": "To identify the differentially expressed genes (DEGs), GSE2549 and GSE51024 MPM datasets were employed. After annotating the probes into gene symbols by the platform annotation files, we used R package LIMMA (Ritchie et al., 2015) to get the DEGs between the tumor and normal tissue following the criteria of adjusted P-value < 0.05, |log2FoldChange| > 1 in both sets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32849853", "locator": "sections[4] \"Differential mRNA Analysis\" paragraph 2", "quote": "To identify the differentially expressed genes (DEGs), GSE2549 and GSE51024 MPM datasets were employed. After annotating the probes into gene symbols by the platform annotation files, we used R package LIMMA (Ritchie et al., 2015) to get the DEGs between the tumor and normal tissue following the criteria of adjusted P-value < 0.05, |log2FoldChange| > 1 in both sets."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2549, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51024, and https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32849853", "locator": "sections[17] \"Data Availability Statement\" paragraph 2", "quote": "Publicly available datasets were analyzed in this study. This data can be found here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2549, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51024, and https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga."}], "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:32849853"], "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. 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After annotating the probes into gene symbols by the platform annotation files, we used R package LIMMA (Ritchie et al., 2015) to get the DEGs between the tumor and normal tissue following the criteria of adjusted P-value < 0.05, |log2FoldChange| > 1 in both sets."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "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-4", "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": ["method.reader_differs_from_extractor"]}, "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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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