Development and Validation of Hub Genes for Adrenal Aldosterone-Producing Adenoma by Integrated Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34984024", "kind": "science-record", "revision": 5, "content_hash": "sha256:3a1dde60ee97a9a58faa5b3f151fade9649a74e74ec5ecc5307d7d88822c24d9", "created_at": "2026-11-01T17:36:41Z", "updated_at": "2026-11-01T22:48:10Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Development and Validation of Hub Genes for Adrenal Aldosterone-Producing Adenoma by Integrated Bioinformatics Analysis.", "doi": "10.2147/IJGM.S330956", "pmid": "34984024", "authors": ["Hai Cai", "Shao-Ming Chen", "Zhi-Bin Ke", "Hang Chen", "Jun-Ming Zhu", "Ting-Ting Lin", "Fei Huang", "Yong Wei", "Qing-Shui Zheng", "Xue-Yi Xue", "Xiong-Lin Sun", "Ning Xu"], "journal": "International journal of general medicine", "year": 2021, "abstract": "OBJECTIVE: To develop and validate hub genes involving in the development and progression of primary aldosteronism (PA) and adrenal aldosterone-producing adenoma (APA).\nMATERIALS AND METHODS: A total of four datasets of gene expression profiles related to APA were downloaded from GEO datasets. GSE60042 and GSE8514 were used to identify DEGs. Weighted gene co-expression network analysis (WGCNA) and protein-protein interaction (PPI) network module analysis were conducted. GO and KEGG enrichment analysis was performed. GSE10927 and GSE33371 were used for further external validation.\nRESULTS: We identified a total of 892 DEGs from GSE60042 and 1167 DEGs from GSE8514. WGCNA analysis demonstrated that the blue module (255 genes) and turquoise module (303 genes) were significantly correlated with APA. PPI networks were then constructed. GO term enrichment analysis suggested that cellular divalent inorganic cation homeostasis, calcium ion homeostasis, collagen-containing extracellular matrix, transport vesicle and metal ion transmembrane transporter activity were the vital annotations. KEGG pathway analysis found that these genes were significantly enriched in neuroactive ligand-receptor interaction, calcium signaling pathway. Finally, we identified a total of 11 candidate genes involving in the development and progression of APA and PA. Besides, two independent datasets (GSE10927 and GSE33371) were used for external validation, and there were seven hub genes successfully verified, including C3, GRM3, AVPR1A, WFS1, PTGFR, NTSR2, and JUN.\nCONCLUSION: These newly identified genes could contribute to the understanding of potential mechanism in APA and PA and might be promising targets for the treatment of APA and PA.", "claims": [{"id": "claim-method", "statement": "R packages “limma” was used to identify DEGs between APA and normal adrenal tissue in GSE60042 and GSE8514. We set false discovery rate (FDR) < 0.05 and |log fold change (FC)| ≥ 1 as the cut-off criterion.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34984024", "locator": "sections[3] \"Microarray Data\" paragraph 2", "quote": "R packages “limma” was used to identify DEGs between APA and normal adrenal tissue in GSE60042 and GSE8514. We set false discovery rate (FDR) < 0.05 and |log fold change (FC)| ≥ 1 as the cut-off criterion."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during the present study was downloaded from GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34984024", "locator": "sections[20] \"Data Sharing Statement\" paragraph 2", "quote": "All data generated or analyzed during the present study was downloaded from GEO database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Two independent datasets were used for external validation, and seven hub genes were successfully verified: C3, GRM3, AVPR1A, WFS1, PTGFR, NTSR2, and JUN.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34984024", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Besides, two independent datasets (GSE10927 and GSE33371) were used for external validation, and there were seven hub genes successfully verified, including C3, GRM3, AVPR1A, WFS1, PTGFR, NTSR2, and JUN."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Two independent datasets were used for external validation, and seven hub genes were successfully verified: C3, GRM3, AVPR1A, WFS1, PTGFR, NTSR2, and JUN.", "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:34984024"], "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:GSE10927"], "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:GSE10927"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34984024", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/IJGM.S330956", "sha256": 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We set false discovery rate (FDR) < 0.05 and |log fold change (FC)| ≥ 1 as the cut-off criterion."}}, {"id": "method-2", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "targets": [], "gaps": []}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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