Comprehensive Analysis Identifies COL1A1, COL3A1, and POSTN as Key Genes Associated with Brain Metastasis in Patients with Breast Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35990840", "kind": "science-record", "revision": 4, "content_hash": "sha256:4e7ae0e5de0ac2cf17197640e0d6b4d0e08f2815fc149d61822e07ad30f20b9b", "created_at": "2026-11-01T18:15:07Z", "updated_at": "2026-11-01T22:07:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive Analysis Identifies COL1A1, COL3A1, and POSTN as Key Genes Associated with Brain Metastasis in Patients with Breast Cancer.", "doi": "10.1155/2022/7812218", "pmid": "35990840", "authors": ["Weidan Wu", "Linlin Zheng"], "journal": "Evidence-based complementary and alternative medicine : eCAM", "year": 2022, "abstract": "Objective: Brain metastasis (BM) is associated with a high mortality in patients with breast cancer (BC). Nevertheless, the molecular mechanisms of BM in BM remain uncertain. The study aims to identify the key genes in BC in relation to BM and to assess their prognostic value.\nMethods: Two microarray datasets GSE125989 and GSE100534 were downloaded from the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs) between primary BC and BM samples. The function enrichment analysis and protein-protein interaction (PPI) network were performed. We mapped hub genes into the Kaplan-Meier database for their correlations with BC survival.\nResults: Venn diagram analysis showed an overlapped upregulated DEG and 18 overlapped downregulated ones between primary BC and BM samples. We constructed the PPI network, and top 5 hub genes were sorted out according to the node degree, including type I collagen α 1 chain (COL1A1), lumican (LUM), type III collagen α 1 chain (COL3A1), type V collagen α 2 chain (COL5A2), and periosteal protein (POSTN). The Kaplan-Meier database analysis found that COL1A1, COL3A1, and POSTN were significantly correlated with overall survival of BC patients.\nConclusion: The study suggests that COL1A1, COL3A1, and POSTN may be key genes associated with BM in patients with BC.", "claims": [{"id": "claim-method", "statement": "To evaluate the prognostic values of 5 hub genes above identified in BC, we mapped them into the Kaplan–Meier database for their correlations with BC survival, with the log-rank test and a 95% hazard ratio (HR) calculated.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35990840", "locator": "sections[12] \"3.4. Prognostic Values of Hub Genes\" paragraph 2", "quote": "To evaluate the prognostic values of 5 hub genes above identified in BC, we mapped them into the Kaplan–Meier database for their correlations with BC survival, with the log-rank test and a 95% hazard ratio (HR) calculated."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study are included within the article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35990840", "locator": "sections[14] \"Data Availability\" paragraph 2", "quote": "The data used to support the findings of this study are included within the article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "COL1A1, COL3A1, and POSTN expression was significantly associated with overall survival in breast cancer patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35990840", "locator": "sections[12] \"3.4. Prognostic Values of Hub Genes\" paragraph 2", "quote": "Among these 5 hub genes, we found the expressions of COL1A1 [HR= 0.72 (0.58–0.91), P=0.005], COL3A1 [HR= 1.28 (1.02–1.6), P=0.031], and POSTN (HR= 0.75 (0.6–0.94), P=0.031) were significantly correlated with overall survival of BC patients (Figure 4), while the expressions of LUM [HR= 0.82 (0.66–1.03), P=0.084] and COL5A2 [HR= 0.95 (0.76–1.19), P=0.66] were not."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "COL1A1, COL3A1, and POSTN expression was significantly associated with overall survival in breast cancer patients.", "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:35990840"], "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:GSE100534"], "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": {"hazard_ratio": "th calculation of a 95% hazard ratio"}, "inputs": ["data:geo:GSE100534"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35990840", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/7812218", 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