Prognostic model of AU-rich genes predicting the prognosis of lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34707942", "kind": "science-record", "revision": 5, "content_hash": "sha256:751d0d290ef2b4da764d03c9197c020b08208ddc55f4d003dc455531c95989f3", "created_at": "2026-11-01T17:36:22Z", "updated_at": "2026-11-01T22:47:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Prognostic model of AU-rich genes predicting the prognosis of lung adenocarcinoma.", "doi": "10.7717/peerj.12275", "pmid": "34707942", "authors": ["Yong Liu", "Zhaofei Pang", "Xiaogang Zhao", "Yukai Zeng", "Hongchang Shen", "Jiajun Du"], "journal": "PeerJ", "year": 2021, "abstract": "BACKGROUND: AU-rich elements (ARE) are vital cis-acting short sequences in the 3'UTR affecting mRNA stability and translation. The deregulation of ARE-mediated pathways can contribute to tumorigenesis and development. Consequently, ARE-genes are promising to predict prognosis of lung adenocarcinoma (LUAD) patients.\nMETHODS: Differentially expressed ARE-genes between LUAD and adjacent tissues in TCGA were investigated by Wilcoxon test. LASSO and Cox regression analyses were performed to identify a prognostic genetic signature. The genetic signature was combined with clinicopathological features to establish a prognostic model. LUAD patients were divided into high- and low-risk groups by the model. Kaplan-Meier curve, Harrell's concordance index (C-index), calibration curves and decision curve analyses (DCA) were used to assess the model. Function enrichment analysis, immunity and tumor mutation analyses were performed to further explore the underlying molecular mechanisms. GEO data were used for external validation.\nRESULTS: Twelve prognostic genes were identified. The gene riskScore, age and stage were independent prognostic factors. The high-risk group had worse overall survival and was less sensitive to chemotherapy and radiotherapy (P < 0.01). C-index and calibration curves showed good performance on survival prediction in both TCGA (1, 3, 5-year ROC: 0.788, 0.776, 0.766) and the GSE13213 validation cohort (1, 3, 5-year ROC: 0.781, 0.811, 0.734). DCA showed the model had notable clinical net benefit. Furthermore, the high-risk group were enriched in cell cycle, DNA damage response, multiple oncological pathways and associated with higher PD-L1 expression, M1 macrophage infiltration. There was no significant difference in tumor mutation burden (TMB) between high- and low-risk groups.\nCONCLUSION: ARE-genes can reliably predict prognosis of LUAD and may become new therapeutic targets for LUAD.", "claims": [{"id": "claim-method", "statement": "Differentially expressed ARE-genes between LUAD and adjacent tissues in TCGA were investigated by Wilcoxon test. LASSO and Cox regression analyses were performed to identify a prognostic genetic signature.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34707942", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Differentially expressed ARE-genes between LUAD and adjacent tissues in TCGA were investigated by Wilcoxon test. LASSO and Cox regression analyses were performed to identify a prognostic genetic signature."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:All data used are available at the TCGA, GEO and ARED databases.The discovery cohort data is available at TCGA (https://portal.gdc.cancer.gov/) (filter criteria: bronchus and lung, TCGA, TCGA-LUAD, transcriptome profiling, Gene Expression Quantification, HTSeq-FPKM).The validation cohort data is available at GEO: GSE13213.The genes coding for AU-rich elements (ARE-genes) are available at the human AU-rich element-containing mRNA database (ARED) (https://brp.kfshrc.edu.sa/ared).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34707942", "locator": "sections[21] \"Additional Information and Declarations\" paragraph 4", "quote": "The following information was supplied regarding data availability:All data used are available at the TCGA, GEO and ARED databases.The discovery cohort data is available at TCGA (https://portal.gdc.cancer.gov/) (filter criteria: bronchus and lung, TCGA, TCGA-LUAD, transcriptome profiling, Gene Expression Quantification, HTSeq-FPKM).The validation cohort data is available at GEO: GSE13213.The genes coding for AU-rich elements (ARE-genes) are available at the human AU-rich element-containing mRNA database (ARED) (https://brp.kfshrc.edu.sa/ared)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Twelve prognostic genes were identified.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34707942", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Twelve prognostic genes were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Twelve prognostic genes were identified.", "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:34707942"], "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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the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8504460", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE13213", "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=GSE13213", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE13213", "version": null, "note": "The following information was supplied regarding data availability:All data used are available at the TCGA, GEO and ARED databases.The discovery cohort data is available at TCGA (https://portal.gdc.cancer.gov/) (filter criteria: bronchus and lung, TCGA, TCGA-LUAD, transcriptome profiling, Gene Expression Quantification, HTSeq-FPKM).The validation cohort data is available at GEO: GSE13213.The genes coding for AU-rich elements (ARE-genes) are available at the human AU-rich element-containing mRNA database (ARED) (https://brp.kfshrc.edu.sa/ared).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:All data used are available at the TCGA, GEO and ARED databases.The discovery cohort data is available at TCGA (https://portal.gdc.cancer.gov/) (filter criteria: bronchus and lung, TCGA, TCGA-LUAD, transcriptome profiling, Gene Expression Quantification, HTSeq-FPKM).The validation cohort data is available at GEO: GSE13213.The genes coding for AU-rich elements (ARE-genes) are available at the human AU-rich element-containing mRNA database (ARED) (https://brp.kfshrc.edu.sa/ared).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM333673", "GSM333674", "GSM333675", "GSM333676", "GSM333677", "GSM333678", "GSM333679", "GSM333680", "GSM333681", "GSM333682", "GSM333683", "GSM333684", "GSM333685", "GSM333686", "GSM333687", "GSM333688", "GSM333689", "GSM333690", "GSM333691", "GSM333692", "GSM333693", "GSM333694", "GSM333695", "GSM333696", "GSM333697", "GSM333698", "GSM333699", "GSM333700", "GSM333701", "GSM333702", "GSM333703", "GSM333704", "GSM333705", "GSM333706", "GSM333707", "GSM333708", "GSM333709", "GSM333710", "GSM333711", "GSM333712", "GSM333713", "GSM333714", "GSM333715", "GSM333716", "GSM333717", "GSM333718", "GSM333719", "GSM333720", "GSM333721", "GSM333722", "GSM333723", "GSM333724", "GSM333725", "GSM333726", "GSM333727", "GSM333728", "GSM333729", "GSM333730", "GSM333731", "GSM333732", "GSM333733", "GSM333734", "GSM333735", "GSM333736", "GSM333737", "GSM333738", "GSM333739", "GSM333740", "GSM333741", "GSM333742", "GSM333743", "GSM333744", "GSM333745", "GSM333746", "GSM333747", "GSM333748", "GSM333749", "GSM333750", "GSM333751", "GSM333752", "GSM333753", "GSM333754", "GSM333755", "GSM333756", "GSM333757", "GSM333758", "GSM333759", "GSM333760", "GSM333761", "GSM333762", "GSM333763", "GSM333764", "GSM333765", "GSM333766", "GSM333767", "GSM333768", "GSM333769", "GSM333770", "GSM333771", "GSM333772", "GSM333773", "GSM333774", "GSM333775", "GSM333776", "GSM333777", "GSM333778", "GSM333779", "GSM333780", "GSM333781", "GSM333782", "GSM333783", "GSM333784", "GSM333785", "GSM333786", "GSM333787", "GSM333788", "GSM333789"], "sample_count": 117, "group_sizes": null, "group_sizes_basis": null, "platform": "6480", "taxon": "Homo sapiens", "title": "Relapse-related molecular signature in lung adenocarcinomas identifies patients with dismal prognosis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE13213 not downloaded", "asset:data:geo:GSE13213 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differentially expressed ARE-genes between LUAD and adjacent tissues in TCGA were investigated by Wilcoxon test. 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