A novel microRNA signature for pathological grading in lung adenocarcinoma based on TCGA and GEO data.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32323746", "kind": "science-record", "revision": 7, "content_hash": "sha256:2ac92a39cabb895a890165433570d9c911474cddbb91d790f55ff580b7c7c853", "created_at": "2026-11-01T15:41:00Z", "updated_at": "2026-11-01T22:01:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "A novel microRNA signature for pathological grading in lung adenocarcinoma based on TCGA and GEO data.", "doi": "10.3892/ijmm.2020.4526", "pmid": "32323746", "authors": ["Zhiyu Yang", "Hongkun Yin", "Lei Shi", "Xiaohua Qian"], "journal": "International journal of molecular medicine", "year": 2020, "abstract": "Lung adenocarcinoma (LUAD) is one of the most common types of lung cancer and its poor prognosis largely depends on the tumor pathological stage. Critical roles of microRNAs (miRNAs) have been reported in the tumorigenesis and progression of lung cancer. However, whether the differential expression pattern of miRNAs could be used to distinguish early‑stage (stage I) from mid‑late‑stage (stages II‑IV) LUAD tumors is still unclear. In this study, clinical information and miRNA expression profiles of patients with LUAD were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus databases. TCGA‑LUAD (n=470) dataset was used for model training and validation, and the GSE62182 (n=94) and GSE83527 (n=36) datasets were used as external independent test datasets. The diagnostic model was created through miRNA feature selection followed by SVM classifier and was confirmed by 5‑fold cross‑validation. A receiver operating characteristic curve was calculated to evaluate the accuracy and robustness of the model. Using the DX score and LIBSVM tool, a 16‑miRNA signature that could distinguish LUAD pathological stages was identified. The area under the curve rates were 0.62 [95% confidence interval (CI): 0.56‑0.67], 0.66 (95% CI: 0.54‑0.76) and 0.63 (95% CI: 0.43‑0.82) in TCGA‑LUAD internal validation dataset, the GSE62182 external validation dataset, and the GSE83527 external validation dataset, respectively. Kyoto Encyclopedia of Genes and Genomes and Gene Ontology enrichment analyses suggested that the target genes of the 16‑miRNA signature were mainly involved in metabolic pathways. The present findings demonstrate that a 16‑miRNA signature could serve as a promising diagnostic biomarker for pathological staging in LUAD.", "claims": [{"id": "claim-method", "statement": "Two-sided Fisher’s exact test was used to analyze the significance of the GO category and KEGG pathway enrichment, and corrected P<0.05 was considered to indicate a statistically significant difference.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32323746", "locator": "sections[5] \"GO and KEGG pathway analyses\" paragraph 2", "quote": "Two-sided Fisher’s exact test was used to analyze the significance of the GO category and KEGG pathway enrichment, and corrected P<0.05 was considered to indicate a statistically significant difference."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data used in this study can be downloaded from TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo) databases.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32323746", "locator": "sections[13] \"Availability of data and materials\" paragraph 2", "quote": "All data used in this study can be downloaded from TCGA (https://portal.gdc.cancer.gov/) and GEO (https://www.ncbi.nlm.nih.gov/geo) databases."}], "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:32323746"], "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:GSE62182"], "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:GSE62182"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32323746", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3892/ijmm.2020.4526", "sha256": 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(23.2)", "23 (24.5)", "15 (41.6)"], ["III", "78 (16.6)", "10 (10.6)", "5 (13.9)"], ["IV", "23 (4.9)", "3 (3.2)", "1 (2.8)"]], "row_count": 12, "column_count": 4, "numeric_cells": 27, "header_rows": 1, "locator": "section[3]/table-wrap[1]#tI-ijmm-45-05-1397"}}, {"id": "asset:table:pmid:32323746:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:31f7bff8be80e875e14f3fc6498a3c303bfa8a43f99b864f8188c4d8406ca682", "bytes": 1022, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[8]/table-wrap[1]#tII-ijmm-45-05-1397", "version": null, "note": "List of the 16 miRNAs in the signature.", "structure": {"pmcid": "PMC7138293", "section_index": 8, "section_title": "miRNA selection, model training and validation", "row_count": 17, "column_count": 3}, "table": {"label": "Table II", "caption": "List of the 16 miRNAs in the signature.", "rows": [["miRNA ID", "miRNA region", "Mature miRNA"], ["hsa-mir-2116", "MIMAT0011161", "hsa-miR-2116-3p"], ["hsa-mir-4661", "MIMAT0019729", "hsa-miR-4661-5p"], ["hsa-mir-3942", "MIMAT0018358", "hsa-miR-3942-5p"], ["hsa-mir-4435", "MIMAT0018951", "hsa-miR-4435"], ["hsa-mir-1307", "MIMAT0005951", "hsa-miR-1307-3p"], ["hsa-mir-1254", "MIMAT0005905", "hsa-miR-1254"], ["hsa-mir-582", "MIMAT0004797", "hsa-miR-582-3p"], ["hsa-mir-5690", "MIMAT0022482", "hsa-miR-5690"], ["hsa-mir-4713", "MIMAT0019821", "hsa-miR-4713-3p"], ["hsa-mir-1293", "MIMAT0005883", "hsa-miR-1293"], ["hsa-mir-939", "MIMAT0004982", "hsa-miR-939-5p"], ["hsa-mir-421", "MIMAT0003339", "hsa-miR-421"], ["hsa-mir-335", "MIMAT0000765", "hsa-miR-335-5p"], ["hsa-mir-4677", "MIMAT0019760", "hsa-miR-4677-5p"], ["hsa-mir-4754", "MIMAT0019894", "hsa-miR-4754"], ["hsa-mir-4746", "MIMAT0019880", "hsa-miR-4746-5p"]], "row_count": 17, "column_count": 3, "numeric_cells": 48, "header_rows": 1, "locator": "section[8]/table-wrap[1]#tII-ijmm-45-05-1397"}}, {"id": "asset:table:pmid:32323746:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:9b4fdee822eb20c7b404b90ab82266f794b80da3618eed56fd5e01cabb5a3e4d", "bytes": 689, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#tIII-ijmm-45-05-1397", "version": null, "note": "Enriched biological pathways identified in a KEGG pathway analysis.", "structure": {"pmcid": "PMC7138293", "section_index": 9, "section_title": "KEGG and GO analyses", "row_count": 7, "column_count": 5}, "table": {"label": "Table III", "caption": "Enriched biological pathways identified in a KEGG pathway analysis.", "rows": [["No.", "KEGG pathway", "P-value", "Genes", "miRNAs"], ["1", "Fatty acid biosynthesis (hsa00061)", "<1x10−325", "1", "4"], ["2", "Fatty acid metabolism (hsa01212)", "<1x10−325", "6", "4"], ["3", "Other glycan degradation (hsa00511)", "9.86x10−06", "3", "2"], ["4", "Steroid biosynthesis (hsa00100)", "6.13x10−05", "13", "2"], ["5", "Biosynthesis of unsaturated fatty acids (hsa01040)", "0.01643741", "4", "2"], ["6", "ECM-receptor interaction (hsa04512)", "0.04934272", "26", "1"]], "row_count": 7, "column_count": 5, "numeric_cells": 30, "header_rows": 1, "locator": "section[9]/table-wrap[1]#tIII-ijmm-45-05-1397"}}, {"id": "asset:table:pmid:32323746:4", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:68b15d1fbc7611c91f149e6cdba87c8cc60c48b84aca25e4876cc7a8c26fb4e8", "bytes": 2568, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[2]#tIV-ijmm-45-05-1397", "version": null, "note": "List of significant GO terms in the biological process category.", "structure": {"pmcid": "PMC7138293", "section_index": 9, "section_title": "KEGG and GO analyses", "row_count": 31, "column_count": 5}, "table": {"label": "Table IV", "caption": "List of significant GO terms in the biological process category.", "rows": [["No.", "GO Term (Biological Process)", "P-value", "Genes", "miRNAs"], ["1", "Biological process (GO:0008150)", "<1x10−325", "1,353", "5"], ["2", "Symbiosis, encompassing mutualism through parasitism (GO:0044403)", "<1x10−325", "94", "5"], ["3", "Gene expression (GO:0010467)", "<1x10−325", "125", "6"], ["4", "Biosynthetic process (GO:0009058)", "<1x10−325", "450", "7"], ["5", "Cellular protein modification process (GO:0006464)", "<1x10−325", "562", "8"], ["6", "Cellular nitrogen compound metabolic process (GO:0034641)", "<1x10−325", "612", "10"], ["7", "Viral process (GO:0016032)", "1.11x10−16", "85", "5"], ["8", "Small molecule metabolic process (GO:0044281)", "1.18x10−14", "552", "5"], ["9", "Neurotrophin TRK receptor signaling pathway (GO:0048011)", "3.90x10−13", "99", "6"], ["10", "Nucleobase-containing compound catabolic process (GO:0034655)", "1.04x10−12", "126", "5"], ["11", "Catabolic process (GO:0009056)", "1.24x10−12", "446", "5"], ["12", "Cellular protein metabolic process (GO:0044267)", "2.49x10−08", "131", "5"], ["13", "Response to stress (GO:0006950)", "7.59x10−08", "511", "5"], ["14", "Blood coagulation (GO:0007596)", "1.66x10−06", "115", "3"], ["15", "Cell death (GO:0008219)", "1.79x10−06", "81", "3"], ["16", "Mitotic cell cycle (GO:0000278)", "1.87x10−06", "60", "5"], ["17", "Membrane organization (GO:0061024)", "1.99x10−06", "93", "5"], ["18", "Fc-epsilon receptor signaling pathway (GO:0038095)", "5.15x10−06", "49", "3"], ["19", "mRNA metabolic process (GO:0016071)", "6.09E-05", "40", "5"], ["20", "Epidermal growth factor receptor signaling pathway (GO:0007173)", "0.000209601", "59", "3"], ["21", "Immune system process (GO:0002376)", "0.000331715", "319", "3"], ["22", "RNA metabolic process (GO:0016070)", "0.000428269", "38", "4"], ["23", "Cellular component assembly (GO:0022607)", "0.000625565", "124", "4"], ["24", "RNA splicing 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