Identification of Atrial Fibrillation-Related lncRNA Based on Bioinformatic Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35154514", "kind": "science-record", "revision": 9, "content_hash": "sha256:bd356c38bbe2c0c0ed0e0bb7a87b40932edc3197f328a7975f3a644424ef7226", "created_at": "2026-11-01T17:36:54Z", "updated_at": "2026-11-01T23:46:27Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Atrial Fibrillation-Related lncRNA Based on Bioinformatic Analysis.", "doi": "10.1155/2022/8307975", "pmid": "35154514", "authors": ["Liangzhen Xie", "GuanShen Huang", "Mingjian Gao", "Jianming Huang", "Hai Li", "Hao Xia", "Xiuting Xiang", "Saizhu Wu", "Yunjun Ruan"], "journal": "Disease markers", "year": 2022, "abstract": "BACKGROUND: Atrial fibrillation (AF) is the most common arrhythmia in the world. Long noncoding RNA (lncRNA) has been found to play an important role in cardiovascular diseases including heart failure, myocardial infarction, and atherosclerosis. However, the role of lncRNA in AF has rarely been studied. The purpose of this study is to identify the expression profile of lncRNA in AF patients, explore the function of lncRNA in AF, and provide a potential scientific basis for the treatment of AF in the future.\nMETHODS: The lncRNA and mRNA expression profiles were obtained from the atrial appendage samples of GSE31821, GSE411774, GSE79768, and GSE115574 in the Gene Expression Omnibus (GEO) database. Functional analysis was performed via Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Variation Analysis (GSVA). The \"CIBERSORT\" R kit was used to analyze 22 immune cell infiltrates in AF and sinus rhythm (SR) patients. The \"CORRPLOT\" R package was used to analyze the immune correlation between lncRNA and immune cells.\nRESULTS: A total of 6 differentially expressed lncRNAs and 45 differentially expressed mRNAs were identified in the AF and SR groups. GO, KEGG, and GSVA results showed that abnormally expressed lncRNAs were involved in signaling pathways related to the atrium, including the Toll-like receptor signaling pathway and calcium signaling pathway. Immune cell infiltration analysis revealed that native B cells, follicular helper T cells, and resting dendritic cells may be involved in the AF process. In addition, LINC00844 was negatively correlated with resting dendritic cells.\nCONCLUSION: The expression profile of lncRNA in AF patients was different from that in normal controls. The physiological functions of these differentially expressed lncRNAs may be related to the pathogenesis of AF, which provide a scientific basis for the prognosis and treatment of patients with AF.", "claims": [{"id": "claim-method", "statement": "In order to evaluate the differential expression, the standard error was adjusted by using the “limma” package of R software, linear model fitting, and a simple empirical Bayes model [16]. For each comparison of each gene, a moderate t statistic and the logarithm of differential expression were calculated. We then adopted the Benjamini and Hochberg (BH) method to adjust the P value to reduce false-positive errors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35154514", "locator": "sections[5] \"2.3. Identification of Differentially Expressed lncRNAs and mRNAs\" paragraph 2", "quote": "In order to evaluate the differential expression, the standard error was adjusted by using the “limma” package of R software, linear model fitting, and a simple empirical Bayes model [16]. For each comparison of each gene, a moderate t statistic and the logarithm of differential expression were calculated. We then adopted the Benjamini and Hochberg (BH) method to adjust the P value to reduce false-positive errors."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35154514", "locator": "sections[22] \"Data Availability\" paragraph 2", "quote": "The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 6 lncRNAs were differentially expressed between the SR group and the AF group, while 45 differentially expressed mRNAs were identified.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "A total of 6 lncRNAs were differentially expressed between the SR group and the AF group (log2FC > 0.58 and P < 0.05), compared with SR groups: 4 lncRNAs were upregulated and 2 were downregulated in AF groups (Figures 2(a) and 2(b))."}, "evidence": [{"asset": "source:pmid:35154514", "locator": "sections[12] \"3.1. Identification of Differentially lncRNA and mRNA Expression Profile\" paragraph 2", "quote": "A total of 6 lncRNAs were differentially expressed between the SR group and the AF group (log2FC > 0.58 and P < 0.05), compared with SR groups: 4 lncRNAs were upregulated and 2 were downregulated in AF groups (Figures 2(a) and 2(b))."}, {"asset": "source:pmid:35154514", "locator": "sections[12] \"3.1. Identification of Differentially lncRNA and mRNA Expression Profile\" paragraph 2", "quote": "In addition, we also found 45 differentially expressed mRNAs, of which 31 mRNAs were downregulated and 14 were upregulated in AR groups compared with SR groups (Figures 3(a) and 3(b))."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 6 lncRNAs were differentially expressed between the SR group and the AF group, while 45 differentially expressed mRNAs were identified.", "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:35154514"], "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:35154514", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1155/2022/8307975", "sha256": "sha256:484e39f88cd165ff0d527cc73800b95711b58807c1336da2d2726c20faa5f904", "bytes": 22341, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1155/2022/8307975", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8837454", "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": "The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3182680", "GSM3182681", "GSM3182682", "GSM3182683", "GSM3182684", "GSM3182685", "GSM3182686", "GSM3182687", "GSM3182688", "GSM3182689", "GSM3182690", "GSM3182691", "GSM3182692", "GSM3182693", "GSM3182694", "GSM3182695", "GSM3182696", "GSM3182697", "GSM3182698", "GSM3182699", "GSM3182700", "GSM3182701", "GSM3182702", "GSM3182703", "GSM3182704", "GSM3182705", "GSM3182706", "GSM3182707", "GSM3182708", "GSM3182709", "GSM3182710", "GSM3182711", "GSM3182712", "GSM3182713", "GSM3182714", "GSM3182715", "GSM3182716", "GSM3182717", "GSM3182718", "GSM3182719", "GSM3182720", "GSM3182721", "GSM3182722", "GSM3182723", "GSM3182724", "GSM3182725", "GSM3182726", "GSM3182727", "GSM3182728", "GSM3182729", "GSM3182730", "GSM3182731", "GSM3182732", "GSM3182733", "GSM3182734", "GSM3182735", "GSM3182736", "GSM3182737", "GSM3182738"], "sample_count": 59, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression data from human left and right atrial tissues in patients with degenerative MR in SR and AFib.", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE31821", "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=GSE31821", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31821", "version": null, "note": "The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets generated for this study can be found in the GEO database (GSE31821, GSE411774, GSSE79768, and GSE115574; https://www.ncbi.nlm.nih.gov/geo/).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM789270", "GSM789271", "GSM789272", "GSM789273", "GSM789274", "GSM789275"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression and miRNA profiles in atrial fibrillation. 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