Investigation of hypoxia networks in ovarian cancer via bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29482638", "kind": "science-record", "revision": 8, "content_hash": "sha256:0071014943f3ecefa8c7de45767d06a505b1a566498e587b9ef239628cbf56f5", "created_at": "2026-11-01T15:40:31Z", "updated_at": "2026-11-01T22:43:17Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Investigation of hypoxia networks in ovarian cancer via bioinformatics analysis.", "doi": "10.1186/s13048-018-0388-x", "pmid": "29482638", "authors": ["Ke Zhang", "Xiangjun Kong", "Guangde Feng", "Wei Xiang", "Long Chen", "Fang Yang", "Chunyu Cao", "Yifei Ding", "Hang Chen", "Mingxing Chu", "Pingqing Wang", "Baoyun Zhang"], "journal": "Journal of ovarian research", "year": 2018, "abstract": "BACKGROUND: Ovarian cancer is a leading cause of the death from gynecologic malignancies. Hypoxia is closely related to the malignant growth of cells. However, the molecular mechanism of hypoxia-regulated ovarian cancer cells remains unclear. Thus, this study was conducted to identify the key genes and pathways implicated in the regulation of hypoxia by bioinformatics analysis.\nMETHODS: Using the datasets of GSE53012 downloaded from the Gene Expression Omnibus (GEO), the differentially expressed genes (DEGs) were screened by comparing the RNA expression from cycling hypoxia group, chronic hypoxia group, and control group. Subsequently, cluster analysis was performed followed by the construction of the protein-protein interaction (PPI) network of the overlapping DEGs between the cycling hypoxia and chronic hypoxia using ClusterONE. In addition, gene ontology (GO) functional and pathway enrichment analyses of the DEGs in the most remarkable module were performed using Database for Annotation, Visualization and Integrated Discovery (DAVID) software. Ultimately, the signaling pathways associated with hypoxia were verified by RT-PCR, WB, and MTT assays.\nRESULTS: A total of 931 overlapping DEGs were identified. Nine hub genes and seven node genes were screened by analyzing the PPI and pathway integration networks, including ESR1, MMP2, ErbB2, MYC, VIM, CYBB, EDN1, SERPINE1, and PDK. Additionally, 11 key pathways closely associated with hypoxia were identified, including focal adhesion, ErbB signaling, and proteoglycans in cancer, among which the ErbB signaling pathway was verified by RT-PCR, WB, and MTT assays. Furthermore, functional enrichment analysis revealed that these genes were mainly involved in the proliferation of ovarian cancer cells, such as regulation of cell proliferation, cell adhesion, positive regulation of cell migration, focal adhesion, and extracellular matrix binding.\nCONCLUSION: The results show that hypoxia can promote the proliferation of ovarian cancer cells by affecting the invasion and adhesion functions through the dysregulation of ErbB signaling, which may be governed by the HIF-1α-TGFA-EGFR-ErbB2-MYC axis. These findings will contribute to the identification of new targets for the diagnosis and treatment of ovarian cancer.", "claims": [{"id": "claim-method", "statement": "Statistical significance was assessed by one-way ANOVA followed by Tukey’s multiple comparisons test using Prism statistical software (GraphPad Software, Inc., La Jolla, CA), with differences considered significant at the level of P < .05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29482638", "locator": "sections[12] \"Statistical analysis\" paragraph 2", "quote": "Statistical significance was assessed by one-way ANOVA followed by Tukey’s multiple comparisons test using Prism statistical software (GraphPad Software, Inc., La Jolla, CA), with differences considered significant at the level of P < .05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study available from the corresponding author on reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29482638", "locator": "sections[26] \"ack\" paragraph 1", "quote": "The datasets used and/or analyzed during the current study available from the corresponding author on reasonable request."}], "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:29482638"], "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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RESULTS: A total of 931 overlapping", "ling pathway was verified by RT-PCR, WB, and MTT assays. Furthermore, functional enrichment a", "to cell proliferation, differentiation, and apoptosis. The proliferation and clone-forming ability"], "order_basis": "paper_text_order:1191", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["llular component (CC) [28]. Cell culture and transfection The human ovarian cancer cell line, Caov3, a", "d interference vectors pSUPER-TGFA/EGFR were transfected using Lipofectamine 2000. 8 h later, cells w"], "order_basis": "paper_text_order:3263", "id": "assay:2"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["gy, cancer hospital of Guizhou province, was cultured in a monolayer in Dulbecco’s modified Eagle’s m"], "order_basis": "paper_text_order:3402", "id": "assay:3"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Statistical significance was assessed by one-way ANOVA followed by Tukey’s multiple comparisons test using Prism statistical software (GraphPad Software, Inc., La Jolla, CA), with differences considered significant at the level of P < .05."], "order_basis": "consumes_earlier_output", "id": "assay:4"}]}