[Identification and validation of hub genes in prostate cancer progression based on weighted gene co-expression network analysis].

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34916188", "kind": "science-record", "revision": 3, "content_hash": "sha256:6d44bd3df40ba451ef7d74e58303daacc4aea7623d0150a42978b51e6c330396", "created_at": "2026-11-01T17:36:37Z", "updated_at": "2026-11-01T21:26:48Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "[Identification and validation of hub genes in prostate cancer progression based on weighted gene co-expression network analysis].", "doi": "10.12122/j.issn.1673-4254.2021.11.06", "pmid": "34916188", "authors": ["H Zhang", "N Chen", "X Wang", "B Gao", "M Ling", "G Chen", "Z Wu", "Y Li", "W Zhong", "B Pan"], "journal": "Nan fang yi ke da xue xue bao = Journal of Southern Medical University", "year": 2021, "abstract": "OBJECTIVE: To identify the key hub genes in prostate cancer metastasis based on weighted gene co-expression network analysis (WGCNA) and verify the identified genes.\nMETHODS: Whole-genome chip data GSE6919 of prostate cancer study were analyzed using principal component analysis (PCA), and the differentially expressed genes (DEGs) were analyzed using R software. WGCNA was performed to construct a gene co-expression network for screening the key genes. TCGA database was used to explore the expressions of the DEGs and their association with the prognosis. To validate the results, we designed siRNA fragments targeting the metastasis-related gene HNRNPA2B1, and observed its effect on growth, apoptosis, clone formation, migration and invasion of prostate cancer cell lines using MTT assay, flow cytometry, clone formation assay, and Transwell assay.\nRESULTS: PCA analysis showed obvious clustering of significant DEGs in metastatic cancer group. The modules obtained by WGCNA analysis in metastasis group involved stem cell differentiation, amino acid metabolism and immune response. Further screening of the genes identified 3 genes related with prostate cancer occurrence (BDH1, PAK4 and EXTL3) and another 3 with prostate cancer metastasis (NKTR, CTBP2 and HNRNPA2B1), which were shown to have differential expressions in TCGA database and were correlated with the patient's overall survival. In the cell experiment, PC3 and LNCap cells transfected with the siRNA fragment targeting HNRNPA2B1 showed obvious growth inhibition with increased cell apoptosis, lowered clone formation ability, and suppressed capacities for migration and invasion.\nCONCLUSION: We identified 3 hub genes related with the occurrence (BDH1, PAK4 and EXTL3) and another 3 with metastasis of prostate cancer (NKTR, CTBP2 and HNRNPA2B1) using WGCNA, which provides a new approach for studying the regulatory mechanisms of prostate cancer.", "claims": [{"id": "claim-method", "statement": "通过加权基因共表达网络分析（WGCNA）挖掘并验证前列腺癌转移的关键枢纽基因。", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34916188", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "通过加权基因共表达网络分析（WGCNA）挖掘并验证前列腺癌转移的关键枢纽基因。"}], "state": "complete"}, {"id": "claim-data-access", "statement": "对前列腺癌全基因组芯片GSE6919进行主成分分析（PCA），通过R语言分析差异表达基因（DEGs）；利用WGCNA构建基因共表达网络并筛选关键基因；在TCGA公共数据中分析基因表达量及其与患者预后的关系；", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34916188", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "对前列腺癌全基因组芯片GSE6919进行主成分分析（PCA），通过R语言分析差异表达基因（DEGs）；利用WGCNA构建基因共表达网络并筛选关键基因；在TCGA公共数据中分析基因表达量及其与患者预后的关系；"}], "state": "complete"}, {"id": "claim-target-result", "statement": "发现前列腺癌发生相关的BDH1、PAK4、EXTL3和转移相关的NKTR、CTBP2、HNRNPA2B1 6个枢纽基因，为前列腺癌调控机制的研究提供了新思路。", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34916188", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "发现前列腺癌发生相关的BDH1、PAK4、EXTL3和转移相关的NKTR、CTBP2、HNRNPA2B1 6个枢纽基因，为前列腺癌调控机制的研究提供了新思路。"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "发现前列腺癌发生相关的BDH1、PAK4、EXTL3和转移相关的NKTR、CTBP2、HNRNPA2B1 6个枢纽基因，为前列腺癌调控机制的研究提供了新思路。", "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:34916188"], "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:GSE6919"], "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:GSE6919"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34916188", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12122/j.issn.1673-4254.2021.11.06", "sha256": 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