Identification of Key Genes Associated with Brain Metastasis from Breast Cancer: A Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35296631", "kind": "science-record", "revision": 5, "content_hash": "sha256:4c53c0e0caece0463628557bed988a62d8d124b92110fc06872098a6c83ee2b9", "created_at": "2026-11-01T18:14:05Z", "updated_at": "2026-11-01T22:48:40Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Key Genes Associated with Brain Metastasis from Breast Cancer: A Bioinformatics Analysis.", "doi": "10.12659/MSM.935071", "pmid": "35296631", "authors": ["Cheng Zeng", "Mingxi Lin", "Yizi Jin", "Jian Zhang"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2022, "abstract": "BACKGROUND As the second most frequent factor of brain metastasis worldwide, breast cancer and its pathogenesis have been researched intensively. Nevertheless, the molecular mechanisms of brain metastasis from breast cancer (BMBC) remain uncertain. The purpose of this study was to explore the key genes concerning the prognosis of BMBC and identify their predictive value. MATERIAL AND METHODS Obtained from the Gene Expression Omnibus (GEO) database, microarray datasets GSE125989, GSE52604, and GSE159956 were used to identify the differentially expressed genes (DEGs) and perform function enrichment analysis. RESULTS Of a total of 240 DEGs, 113 genes were upregulated and 127 genes were downregulated. The protein-protein interaction (PPI) was performed through STRING, and 29 hub genes were screened through Cytoscape. After being examined through the cBioportal online platform and the Oncomine database, 8 key genes were finally obtained, including COL14A1, COL3A1, COL6A3, THY1, MMP14, GAP43, PTPRN, and SNAP25. In the validation dataset GSE46928, COL14A1 was shown to have predictive significance of brain metastasis in breast cancer. CONCLUSIONS The key genes explored in this article could assist in identifying the molecular mechanism of BMBC. Also, COL14A1, COL3A1, COL6A3, THY1, MMP14, GAP43, PTPRN, and SNAP25 might be candidate targets for diagnosis and treatment of BMBC, and COL3A1 might have predictive value.", "claims": [{"id": "claim-method", "statement": "The differentially expressed genes (DEGs) between primary breast cancer and BMBC were inspected by the LIMMA package of R in datasets GSE125989 and GSE52604. The Kaplan-Meier curve on the cBioPortal (http://www.cbioportal.org) online platform and the box line diagram on the Oncomine database (http://www.oncomine.com) were used to explore the relationship between expression patterns and metastasis and to determine the final hub genes.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35296631", "locator": "sections[4] \"Identification of Differentially Expressed Genes\" paragraph 2", "quote": "The differentially expressed genes (DEGs) between primary breast cancer and BMBC were inspected by the LIMMA package of R in datasets GSE125989 and GSE52604."}, {"asset": "source:pmid:35296631", "locator": "sections[7] \"Survival Analysis and Hub Genes Selection\" paragraph 2", "quote": "The Kaplan-Meier curve on the cBioPortal (http://www.cbioportal.org) online platform and the box line diagram on the Oncomine database (http://www.oncomine.com) were used to explore the relationship between expression patterns and metastasis and to determine the final hub genes."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from GEO (http://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35296631", "locator": "sections[18] \"fn-group\" paragraph 1", "quote": "The datasets used and/or analyzed during the current study are available from GEO (http://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Eight key genes were identified as potential biomarkers for brain metastasis from breast cancer, and COL3A1 was statistically significant in predicting brain metastasis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35296631", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "After being examined through the cBioportal online platform and the Oncomine database, 8 key genes were finally obtained, including COL14A1, COL3A1, COL6A3, THY1, MMP14, GAP43, PTPRN, and SNAP25."}, {"asset": "source:pmid:35296631", "locator": "sections[14] \"Validation Study\" paragraph 2", "quote": "Finally, to judge the predictive value of the 8 identified hub genes, we performed survival analysis on the GSE159956 dataset and found that COL3A1 was statistically significant, as shown in Figure 7."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Eight key genes were identified as potential biomarkers for brain metastasis from breast cancer, and COL3A1 was statistically significant in predicting brain metastasis.", "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:35296631"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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