Mining of Potential Biomarkers and Pathway in Valvular Atrial Fibrillation (VAF) via Systematic Screening of Gene Coexpression Network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36226239", "kind": "science-record", "revision": 4, "content_hash": "sha256:fd11498f8242e44a9dc7d05971c01b5f4fe60e068b18653e3ef23116cb907827", "created_at": "2026-11-01T18:15:35Z", "updated_at": "2026-11-01T22:07:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Mining of Potential Biomarkers and Pathway in Valvular Atrial Fibrillation (VAF) via Systematic Screening of Gene Coexpression Network.", "doi": "10.1155/2022/3645402", "pmid": "36226239", "authors": ["Fan Zou", "Tiantian Chen", "Xiuying Xiang", "Chengjiang Peng", "Shuai Huang", "Shaohong Ma"], "journal": "Computational and mathematical methods in medicine", "year": 2022, "abstract": "Purpose: We apply the bioinformatics method to excavate the potential genes and therapeutic targets associated with valvular atrial fibrillation (VAF).\nMethods: The downloaded gene expression files from the gene expression omnibus (GEO) included patients with primary severe mitral regurgitation complicated with sinus or atrial fibrillation rhythm. Subsequently, the differential gene expression in left and right atrium was analyzed by R software. Additionally, weighted correlation network analysis (WGCNA), principal component analysis (PCA), and linear model for microarray data (LIMMA) algorithm were used to determine hub genes. Then, Metascape database, DAVID database, and STRING database were used to annotate and visualize the gene ontology (GO) analysis, KEGG pathway enrichment analysis, and PPI network analysis of differentially expressed genes (DEGs). Finally, the TFs and miRNAs were predicted by using online tools, such as PASTAA and miRDB.\nResults: 20,484 differentially expressed genes related to atrial fibrillation were obtained through the analysis of left and right atrial tissue samples of GSE115574 gene chip, and 1,009 were with statistical significance, including 45 upregulated genes and 964 downregulated genes. And the hub genes implicated in AF of NPC2, ODC1, SNAP29, LAPTM5, ST8SIA5, and FCGR3B were screened. Finally, the main regulators of targeted candidate biomarkers and microRNAs, EIF5A2, HIF1A, ZIC2, ELF1, and STAT2, were found in this study.\nConclusion: These hub genes, NPC2, ODC1, SNAP29, LAPTM5, ST8SIA5, and FCGR3B, are important for the development of VAF, and their enrichment pathways and TFs elucidate the involved molecular mechanisms and assist in the validation of drug targets.", "claims": [{"id": "claim-data-access", "statement": "We downloaded these data from the Public Resource Database GEO (http://www.ncbi.nlm.nih.gov/geo/) and generated expression profiling arrays using Affymetrix Human Genome U133 Plus 2 GPL570 (HG-U133_Plus_2). The retrieval involved the following process: (1) collecting datasets searched with the keywords “atrial fibrillation” and “valvular disease”. (2) Select “Homo sapiens” as the specimen source and “Expression profiling by high throughput sequencing” as the study type. (3) The gene chip data is selected as “Affymetrix Human Genome” on the test platform. The GSE115574 dataset was published on September 4, 2019, from surgically resected left and right atrial tissue from 30 patients with severe chronic mitral regurgitation, including 15 with preoperative atrial fibrillation and 15 with preoperative sinus.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36226239", "locator": "sections[3] \"2.1. Materials\" paragraph 2", "quote": "We downloaded these data from the Public Resource Database GEO (http://www.ncbi.nlm.nih.gov/geo/) and generated expression profiling arrays using Affymetrix Human Genome U133 Plus 2 GPL570 (HG-U133_Plus_2). The retrieval involved the following process: (1) collecting datasets searched with the keywords “atrial fibrillation” and “valvular disease”. (2) Select “Homo sapiens” as the specimen source and “Expression profiling by high throughput sequencing” as the study type. (3) The gene chip data is selected as “Affymetrix Human Genome” on the test platform. The GSE115574 dataset was published on September 4, 2019, from surgically resected left and right atrial tissue from 30 patients with severe chronic mitral regurgitation, including 15 with preoperative atrial fibrillation and 15 with preoperative sinus."}], "state": "complete"}, {"id": "claim-target-result", "statement": "20,484 differentially expressed genes related to atrial fibrillation were obtained through the analysis of left and right atrial tissue samples of GSE115574 gene chip, and 1,009 were with statistical significance, including 45 upregulated genes and 964 downregulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36226239", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "20,484 differentially expressed genes related to atrial fibrillation were obtained through the analysis of left and right atrial tissue samples of GSE115574 gene chip, and 1,009 were with statistical significance, including 45 upregulated genes and 964 downregulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "20,484 differentially expressed genes related to atrial fibrillation were obtained through the analysis of left and right atrial tissue samples of GSE115574 gene chip, and 1,009 were with statistical significance, including 45 upregulated genes and 964 downregulated genes.", "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:36226239"], "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:GSE115574"], "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:GSE115574"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36226239", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/3645402", "sha256": "sha256:6216823cc6dfe43beab980c48a3b986f83948f980c104e53ff1a0f343c99a4bf", "bytes": 33677, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/3645402", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9550484", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE115574", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE115574", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE115574", "version": null, "note": "We downloaded these data from the Public Resource Database GEO (http://www.ncbi.nlm.nih.gov/geo/) and generated expression profiling arrays using Affymetrix Human Genome U133 Plus 2 GPL570 (HG-U133_Plus_2). The retrieval involved the following process: (1) collecting datasets searched with the keywords “atrial fibrillation” and “valvular disease”. (2) Select “Homo sapiens” as the specimen source and “Expression profiling by high throughput sequencing” as the study type. (3) The gene chip data is selected as “Affymetrix Human Genome” on the test platform. The GSE115574 dataset was published on September 4, 2019, from surgically resected left and right atrial tissue from 30 patients with severe chronic mitral regurgitation, including 15 with preoperative atrial fibrillation and 15 with preoperative sinus.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded these data from the Public Resource Database GEO (http://www.ncbi.nlm.nih.gov/geo/) and generated expression profiling arrays using Affymetrix Human Genome U133 Plus 2 GPL570 (HG-U133_Plus_2). The retrieval involved the following process: (1) collecting datasets searched with the keywords “atrial fibrillation” and “valvular disease”. (2) Select “Homo sapiens” as the specimen source and “Expression profiling by high throughput sequencing” as the study type. (3) The gene chip data is selected as “Affymetrix Human Genome” on the test platform. 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