Comprehensive analysis of TPX2-related ceRNA network as prognostic biomarkers in lung adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33029085", "kind": "science-record", "revision": 8, "content_hash": "sha256:5847016bc9dd5d766462e2c32907a3964debc643181124360580d6221500d7e8", "created_at": "2026-11-01T15:41:12Z", "updated_at": "2026-11-01T22:02:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive analysis of TPX2-related ceRNA network as prognostic biomarkers in lung adenocarcinoma.", "doi": "10.7150/ijms.49053", "pmid": "33029085", "authors": ["Chen Huo", "Meng-Yu Zhang", "Rui Li", "Xi-Jia Zhou", "Ting-Ting Liu", "Jian-Ping Li", "Xiao Liu", "Yi-Qing Qu"], "journal": "International journal of medical sciences", "year": 2020, "abstract": "Background and aim: Competing endogenous RNA (ceRNA) is believed to play vital roles in tumorigenesis. The goal of this study was to screen prognostic biomarkers in lung adenocarcinoma (LUAD). Methods: Common differentially expressed genes (DEGs) were collected from Gene Expression Omnibus (GEO) databases and The Cancer Genome Atlas databases (TCGA) using GEO2R and \"limma\" package in R, respectively. Overlapping DEGs were conducted using enrichment of functions and protein-protein interaction (PPI) network to discover significant candidate genes. By using a comprehensive analysis, we constructed an mRNA mediated ceRNA network. Survival rates were used Kaplan-Meier analysis. Statistical analysis was used to further identify the prognosis of studied genes. Results: Integrated analysis of GSE32863 and TCGA databases, a total of 886 overlapping DEGs, including 279 up-regulated and 607 down-regulated genes were identified. Considering the highest term of candidate genes in PPI, we identified TPX2, which was enriched in cell division signaling pathway. Besides, 35 differentially expressed miRNAs (DEmiRNAs) were predicted to target TPX2 and only 7 DEmiRNAs were identified to be prognostic biomarkers in LUAD. Then, 30 differentially expressed lncRNAs (DElncRNAs) were predicted to bind these 7 DEmiRNAs. Finally, we found that 7 DElncRNAs were correlated with the overall survival (all p <0.05). Furthermore, we identified elevated TPX2 was strongly correlated with the worse survival rate among 458 samples. Univariate and multivariate cox analysis showed TPX2 may act as an independent factor for prognosis in LUAD (p <0.05). Then pathway enrichment results suggested that TPX2 may facilitate tumorigenesis by participating in several cancer-related signaling pathways in LUAD, especially in Notch signal pathway. Conclusions: TPX2-related lncRNAs and miRNAs are related to the survival of LUAD. 7 lncRNAs, 7 miRNAs and TPX2 may serve as prognostic biomarkers in LUAD.", "claims": [{"id": "claim-method", "statement": "The survival R packages were performed for survival analysis of TPX2 and survival curve was displayed by Kaplan-Meier plotter and examined by log-rank test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33029085", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "The survival R packages were performed for survival analysis of TPX2 and survival curve was displayed by Kaplan-Meier plotter and examined by log-rank test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profile of GSE32863 based on the GPL6884 platform, was selected from Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) 25. GSE32863 included 58 pairs of LUAD and normal lung tissues, normalized microarray data was reanalyzed using the GEO2R online tools (https://www.ncbi.nlm.nih.gov/geo/geo2r/) 26.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33029085", "locator": "sections[3] \"Data collection and significant differentially expressed RNAs screening\" paragraph 2", "quote": "The gene expression profile of GSE32863 based on the GPL6884 platform, was selected from Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) 25. GSE32863 included 58 pairs of LUAD and normal lung tissues, normalized microarray data was reanalyzed using the GEO2R online tools (https://www.ncbi.nlm.nih.gov/geo/geo2r/) 26."}], "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:33029085"], "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:GSE32863"], "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:GSE32863"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33029085", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7150/ijms.49053", "sha256": "sha256:c48897c643b9b95feb067320f4fb20c9a9318d00aa5699f9c8c9615bfd7084d7", "bytes": 38577, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7150/ijms.49053", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7532481", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE32863", "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=GSE32863", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE32863", "version": null, "note": "The gene expression profile of GSE32863 based on the GPL6884 platform, was selected from Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) 25. GSE32863 included 58 pairs of LUAD and normal lung tissues, normalized microarray data was reanalyzed using the GEO2R online tools (https://www.ncbi.nlm.nih.gov/geo/geo2r/) 26.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The gene expression profile of GSE32863 based on the GPL6884 platform, was selected from Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) 25. 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"cell division", "KIFC1, CDCA8, CCNB2, CDCA7, TIMELESS, NEK2, CCNF, TPX2, KNTC1, CENPF, BIRC5, AURKA, CDC20, PTTG1, UBE2C, CDCA5", "1.44E-13"], ["BP", "GO:0007067", "mitotic nuclear division", "CCNB2, TIMELESS, NEK2, CCNF, KNTC1, TPX2, CENPF, AURKA, BIRC5, CDC20, PTTG1, AURKB, CDCA5, ASPM", "1.03E-12"], ["CC", "GO:0005634", "nucleus", "KIFC1, PRC1, NEK2, KNTC1, AURKA, PTTG1, AURKB, TYMS, CDC45, CDCA8, CDCA7, TOP2A, CDCA5, ASPM, FEN1, TRIP13, GINS2, CCNF, TPX2, NUSAP1, CENPF, RMI2, BIRC5, CDC20, MCM2, ECT2, MCM4, UHRF1, CCNB2, TIMELESS, MELK, UBE2T", "1.01E-10"], ["CC", "GO:0005819", "spindle", "KIFC1, PRC1, TPX2, NUSAP1, CENPF, AURKA, BIRC5, CDC20, AURKB, KIF20A", "9.10E-10"], ["CC", "GO:0030496", "midbody", "CDCA8, PRC1, NEK2, CENPF, AURKA, BIRC5, AURKB, ECT2, ASPM, KIF20A", "1.63E-09"]], "row_count": 6, "column_count": 5, "numeric_cells": 15, "header_rows": 1, "locator": "section[11]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:33029085:2", "role": "table", "format": "jats-table", 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14, "section_title": "Prognostic significance of TPX2 in LUAD", "row_count": 9, "column_count": 5}, "table": {"label": "Table 4", "caption": "Univariate and multivariate analysis of prognostic factors in LUAD", "rows": [["Variables", "Univariate analysis", "Multivariate analysis"], ["Hazard ratio (95% CI)", "p value", "Hazard ratio (95%CI)", "p value"], ["Age", "1.002 (0.983-1.021)", "0.843", "", ""], ["Gender", "1.035 (0.717-1.495)", "0.852", "", ""], ["Stage", "1.654 (1.401-1.951)", "<0.01", "1.408 (1.121-1.768)", "0.003"], ["T", "1.632 (1.315-2.024)", "<0.01", "1.238 (0.983-1.560)", "0.070"], ["M", "1.757 (0.964-3.203)", "0.066", "", ""], ["N", "1.790 (1.459-2.196)", "<0.01", "1.201 (0.922-1.564)", "0.174"], ["TPX2", "1.010 (1.003-1.017)", "0.003", "1.218 (1.054-1.4077)", "0.007"]], "row_count": 9, "column_count": 5, "numeric_cells": 24, "header_rows": 2, "locator": "section[14]/table-wrap[1]#T4"}}, {"id": "asset:table:pmid:33029085:5", "role": "table", "format": "jats-table", 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The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE32863"], "resolved_accessions": ["GSE32863"], "statements": ["The gene expression profile of GSE32863 based on the GPL6884 platform, was selected from Gene Expression Omnibus (GEO) (http://www.ncbi.nlm.nih.gov/geo/) 25. GSE32863 included 58 pairs of LUAD and normal lung tissues, normalized microarray data was reanalyzed using the GEO2R online tools (https://www.ncbi.nlm.nih.gov/geo/geo2r/) 26."], "basis": "The paper names GSE32863 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. 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