Identification of genes and analysis of prognostic values in nonsmoking females with non-small cell lung carcinoma by bioinformatics analyses.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30349363", "kind": "science-record", "revision": 8, "content_hash": "sha256:4b7cbdb4252194ef4a99228a666c858cf18fdf397bee4d44f832bfd6f18d6123", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T22:00:06Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of genes and analysis of prognostic values in nonsmoking females with non-small cell lung carcinoma by bioinformatics analyses.", "doi": "10.2147/CMAR.S174409", "pmid": "30349363", "authors": ["Guangda Yang", "Qianya Chen", "Jieming Xiao", "Hailiang Zhang", "Zhichao Wang", "Xiangan Lin"], "journal": "Cancer management and research", "year": 2018, "abstract": "BACKGROUND: This study was performed to identify disease-related genes and analyze prognostic values in nonsmoking females with non-small cell lung carcinoma (NSCLC).\nMATERIALS AND METHODS: Gene expression profile GSE19804 was downloaded from the Gene Expression Omnibus (GEO) database and analyzed by using GEO2R. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes were used for the functional and pathway enrichment analysis. Then, the Search Tool for the Retrieval of Interacting Genes, Cytoscape, and Molecular Complex Detection were used to construct the protein-protein interaction (PPI) network and identify hub genes. Finally, the Kaplan-Meier plotter online tool was used for the overall survival analysis of hub genes.\nRESULTS: A cohort of 699 differentially expressed genes was screened, and they were mainly enriched in the terms of ECM-receptor interaction, focal adhesion, and cell adhesion molecules. A PPI network was constructed, and 15 hub genes were identified base on the subset of PPI network. Then, two significant modules were detected and several genes were found to be associated with the cell cycle pathway. Finally, nine hub genes' (UBE2C, DLGAP5, TPX2, CCNB2, BIRC5, KIF20A, TOP2A, GNG11, and ANXA1) expressions were found to be associated with the prognosis of the patients.\nCONCLUSION: Overall, we propose that the cell cycle pathway may play an important role in nonsmoking females with NSCLC and the nine hub genes may be further explored as potential targets for NSCLC diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "The DEGs between NSCLC samples and normal controls were identified using GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/), which is a web tool that is applied to screen DEGs by comparing two groups of samples. |log FC| >1.5 and P<0.01 were selected as the cutoff criterion.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30349363", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The DEGs between NSCLC samples and normal controls were identified using GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/), which is a web tool that is applied to screen DEGs by comparing two groups of samples. |log FC| >1.5 and P<0.01 were selected as the cutoff criterion."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Gene expression profile GSE19804 was downloaded from the Gene Expression Omnibus (GEO) database and analyzed by using GEO2R. GSE19804, which was based on the platform of the GPL570 (Affymetrix Human Genome U133 Plus 2.0 Array, Santa Clara, CA, USA), consisted of 60 samples from nonsmoking female NSCLC patients and 60 normal samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30349363", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Gene expression profile GSE19804 was downloaded from the Gene Expression Omnibus (GEO) database and analyzed by using GEO2R."}, {"asset": "source:pmid:30349363", "locator": "sections[3] \"Microarray data\" paragraph 2", "quote": "GSE19804, which was based on the platform of the GPL570 (Affymetrix Human Genome U133 Plus 2.0 Array, Santa Clara, CA, USA), consisted of 60 samples from nonsmoking female NSCLC patients and 60 normal samples."}], "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:30349363"], "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:GSE19804"], "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:GSE19804"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:30349363", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/CMAR.S174409", "sha256": "sha256:4536d01de4b199e917f734639d911d37433214e3b94e3a6b7dc51ba29e73b5a7", "bytes": 25870, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/CMAR.S174409", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6183654", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE19804", "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=GSE19804", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE19804", "version": null, "note": "Gene expression profile GSE19804 was downloaded from the Gene Expression Omnibus (GEO) database and analyzed by using GEO2R. 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"structure": {"pmcid": "PMC6183654", "section_index": 11, "section_title": "Construction of PPI network and module identification", "row_count": 17, "column_count": 3}, "table": {"label": "Table 2", "caption": "The hub genes that had a degree >20 in PPI network", "rows": [["Gene", "Regulation", "Degree"], ["", "", ""], ["GNG11", "Down", "29"], ["UBE2C", "Up", "28"], ["CCNB2", "Up", "23"], ["NMU", "Up", "22"], ["ANXA1", "Down", "22"], ["FPR2", "Down", "22"], ["KIF20A", "Up", "22"], ["MELK", "Up", "21"], ["NUSAP1", "Up", "21"], ["DLGAP5", "Up", "21"], ["CENPF", "Up", "21"], ["BIRC5", "Up", "21"], ["TOP2A", "Up", "21"], ["TPX2", "Up", "21"], ["HMMR", "Up", "21"]], "row_count": 17, "column_count": 3, "numeric_cells": 17, "header_rows": 1, "locator": "section[11]/table-wrap[1]#t2-cmar-10-4287"}}, {"id": "asset:table:pmid:30349363:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": 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