Construction of a specific SVM classifier and identification of molecular markers for lung adenocarcinoma based on lncRNA-miRNA-mRNA network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29872324", "kind": "science-record", "revision": 9, "content_hash": "sha256:68581c847681bb39ce28f6f690267a547283e9b62f3a4fac6f89cd1b9b6f943c", "created_at": "2026-11-01T15:40:34Z", "updated_at": "2026-11-01T22:43:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Construction of a specific SVM classifier and identification of molecular markers for lung adenocarcinoma based on lncRNA-miRNA-mRNA network.", "doi": "10.2147/OTT.S151121", "pmid": "29872324", "authors": ["Jingming Zhao", "Wei Cheng", "Xigang He", "Yanli Liu", "Ji Li", "Jiaxing Sun", "Jinfeng Li", "Fangfang Wang", "Yufang Gao"], "journal": "OncoTargets and therapy", "year": 2018, "abstract": "BACKGROUND: Novel diagnostic predictors and drug targets are needed for LUAD (lung adenocarcinoma). We aimed to build a specific SVM (support vector machine) classifier for diagnosis of LUAD and identify molecular markers with prognostic value for LUAD.\nMETHODS: The expression differences of miRNAs, lncRNAs and mRNAs between LUAD and normal samples were compared using data from TCGA (The Cancer Genome Atlas) database. A LUAD related miRNA-lncRNA-mRNA network was constructed, based on which feature genes were selected for the construction of LUAD specific SVM classifier. The robustness and transferability of SVM classifier were validated using gene expression profile datasets GSE43458 and GSE10072. Prognostic markers were identified from the network. A set of LUAD-related differentially expressed miRNAs, lncRNAs and miRNAs were identified and a LUAD related miRNA-lncRNA-mRNA network was obtained. The LUAD specific SVM classifier constructed on the basis of the network was robust and efficient for classification of samples from TCGA dataset and two independent validation datasets.\nRESULTS: Eight RNAs with prognostic value were identified, including hsa-miR-96, hsa-miR-204, PGM5P2 (phosphoglucomutase 5 pseudogene 2), SFTA1P (surfactant associated 1), RGS20 (regulator of G protein signaling 20), RGS9BP (RGS9-binding protein), FGB (fibrinogen beta chain) and INA (alpha-internexin). Among them, RGS20 and INA were regulated by hsa-miR-96. RGS20 was also regulated by hsa-miR-204, which was a potential target of SFTA1P.\nCONCLUSION: The LUAD specific SVM classifier may serve as a novel diagnostic predictor. hsa-miR-96, hsa-miR-204, PGM5P2, SFTA1P, RGS20, RGS9BP, FGB and INA may serve as prognostic markers in clinical practice.", "claims": [{"id": "claim-method", "statement": "Expression differences of mRNAs and miRNA-seq data between LUAD and normal samples were analyzed using edgeR package18 under R3.0.1 and FDR (false discovery rate) was calculated using multtest package.19", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29872324", "locator": "sections[4] \"Identification of LUAD related lncRNAs, miRNAs and mRNAs\" paragraph 2", "quote": "Expression differences of mRNAs and miRNA-seq data between LUAD and normal samples were analyzed using edgeR package18 under R3.0.1 and FDR (false discovery rate) was calculated using multtest package.19"}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mRNA and miRNA expression data of LUAD-related samples was downloaded from TCGA (https://gdc-portal.nci.nih.gov/). After checking the barcode information of samples, a total of 464 LUAD samples with both mRNA and miRNA data were obtained for subsequent analysis, including 445 LUAD and 19 normal samples. All the clinical information related to these samples was also obtained.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29872324", "locator": "sections[3] \"Data source and data preprocessing\" paragraph 2", "quote": "The mRNA and miRNA expression data of LUAD-related samples was downloaded from TCGA (https://gdc-portal.nci.nih.gov/). After checking the barcode information of samples, a total of 464 LUAD samples with both mRNA and miRNA data were obtained for subsequent analysis, including 445 LUAD and 19 normal samples. All the clinical information related to these samples was also obtained."}], "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:29872324"], "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:GSE10072"], "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:GSE10072"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29872324", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/OTT.S151121", "sha256": "sha256:432c70e497f9230912ad14f4a1a5419d25b6f4cbc4b32d5731de514c0887f9da", "bytes": 25595, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/OTT.S151121", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC5975616", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE10072", "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=GSE10072", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE10072", "version": null, "note": "The mRNA and miRNA expression data of LUAD-related samples was downloaded from TCGA (https://gdc-portal.nci.nih.gov/). After checking the barcode information of samples, a total of 464 LUAD samples with both mRNA and miRNA data were obtained for subsequent analysis, including 445 LUAD and 19 normal samples. All the clinical information related to these samples was also obtained.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mRNA and miRNA expression data of LUAD-related samples was downloaded from TCGA (https://gdc-portal.nci.nih.gov/). After checking the barcode information of samples, a total of 464 LUAD samples with both mRNA and miRNA data were obtained for subsequent analysis, including 445 LUAD and 19 normal samples. 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