Development and validation of a RNA binding protein-associated prognostic model for lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32087603", "kind": "science-record", "revision": 9, "content_hash": "sha256:9459ce5bf19913de5202c1dfbfb5b967b49d5cc126167336490843612d3a711c", "created_at": "2026-11-01T15:40:56Z", "updated_at": "2026-11-01T22:44:35Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development and validation of a RNA binding protein-associated prognostic model for lung adenocarcinoma.", "doi": "10.18632/aging.102828", "pmid": "32087603", "authors": ["Wei Li", "Li-Na Gao", "Pei-Pei Song", "Chong-Ge You"], "journal": "Aging", "year": 2020, "abstract": "RNA binding proteins (RBPs) dysregulation have been reported in various malignant tumors and associated with the occurrence and development of cancer. However, the role of RBPs in lung adenocarcinoma (LUAD) is poorly understood. We downloaded the RNA sequencing data of LUAD from the Cancer Genome Atlas (TCGA) database and determined the differently expressed RBPs between normal and cancer tissues. The study then systemically investigated the expression and prognostic value of these RBPs by a series of bioinformatics analysis. A total of 223 differently expressed RBPs were identified, including 101 up-regulated and 122 down-regulated RBPs. Eight RBPs (IGF2BP1, IFIT1B, PABPC1, TLR8, GAPDH, PIWIL4, RNPC3, and ZC3H12C) were identified as prognosis related hub gene and used to construct a prognostic model. Further analysis indicated that the patients in the high-risk subgroup had poor overall survival(OS) compared to those in low-risk subgroup based on the model. The area under the curve of the time-dependent receiver operator characteristic curve of the prognostic model are 0.775 in TCGA cohort and 0.814 in GSE31210 cohort, confirming a good prognostic model. We also established a nomogram based on eight RBPs mRNA and internal validation in the TCGA cohort, which displayed a favorable discriminating ability for lung adenocarcinoma.", "claims": [{"id": "claim-data-access", "statement": "We downloaded the RNA-sequencing dataset of 59 normal lung tissue samples and 524 LUAD samples with corresponding clinical data from The Cancer Genome Atlas database (TCGA, https://portal.gdc.cancer.gov/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32087603", "locator": "sections[12] \"Data processing\" paragraph 2", "quote": "We downloaded the RNA-sequencing dataset of 59 normal lung tissue samples and 524 LUAD samples with corresponding clinical data from The Cancer Genome Atlas database (TCGA, https://portal.gdc.cancer.gov/)."}], "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:32087603"], "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:GSE31210"], "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:GSE31210"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32087603", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/aging.102828", "sha256": "sha256:02dee1f2d03d642bcd8ede08831fcc30efd1f96e4eede5a2fa09fcfd505130ca", "bytes": 38172, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.18632/aging.102828", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7066909", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE31210", "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=GSE31210", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31210", "version": null, "note": "We downloaded the RNA-sequencing dataset of 59 normal lung tissue samples and 524 LUAD samples with corresponding clinical data from The 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"Table 3", "caption": "The prognostic value of different clinical parameters.", "rows": [["", "Univariate analysis", "", "Multivariate analysis"], ["HR", "95% CI", "P-value", "HR", "95%CI", "P-value"], ["Age", "1.02", "0.99-1.03", "0.154", "", "1.03", "1.01-1.05", "0.002"], ["Gender", "1.02", "0.70-1.49", "0.909", "", "0.88", "0.59-1.31", "0.536"], ["Smoking", "0.98", "0.82-1.17", "0.814", "", "1.04", "0.87-1.24", "0.661"], ["Stage", "1.60", "1.35-1.89", "<0.001", "", "1.50", "1.20-1.88", "<0.001"], ["T", "1.48", "1.17-1.88", "<0.001", "", "1.08", "0.83-1.41", "0.551"], ["N", "1.44", "1.23-1.69", "<0.001", "", "1.16", "0.94-1.43", "0.181"], ["M", "1.05", "0.85-1.30", "0.623", "", "1.11", "0.88-1.38", "0.375"], ["Risk score", "1.21", "1.15-1.27", "<0.001", "", "1.26", "1.19-1.34", "<0.001"]], "row_count": 10, "column_count": 8, "numeric_cells": 50, "header_rows": 0, "locator": "section[8]/table-wrap[1]#t3"}}], "gaps": ["asset:data:geo:GSE31210 not downloaded", "asset:data:geo:GSE31210 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with corresponding clinical data from The Cancer Genome Atlas database (TCGA, https://portal.gdc.cancer.gov/).”"}}, {"id": "method-2", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "pathway enrichment"}}], "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", 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