Identification of circRNA-miRNA-mRNA Regulatory Network and Autophagy Interaction Network in Atrial Fibrillation Based on Bioinformatics Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34848999", "kind": "science-record", "revision": 5, "content_hash": "sha256:0b6a591b2ec35a86a9a0fd0c749a370953e706ee1cd8acd7263b998f9c40e311", "created_at": "2026-11-01T17:36:32Z", "updated_at": "2026-11-01T22:47:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of circRNA-miRNA-mRNA Regulatory Network and Autophagy Interaction Network in Atrial Fibrillation Based on Bioinformatics Analysis.", "doi": "10.2147/IJGM.S333752", "pmid": "34848999", "authors": ["Xiaoying Chao", "Weiran Dai", "Shuo Li", "Chenyang Jiang", "Zhiyuan Jiang", "Guoqiang Zhong"], "journal": "International journal of general medicine", "year": 2021, "abstract": "BACKGROUND: Circular RNA (circRNA) has been receiving increased attention in the research of atrial fibrillation (AF). Our study aims to find potential circRNAs and identify the circRNA-miRNA-mRNA regulatory network in AF based on bioinformatics analysis.\nMETHODS: GSE129409 was retrieved from the Gene Expression Omnibus (GEO) database, and we used R software to analyze the differentially expressed circRNAs (DECs). Subsequently, we used several bioinformatics methods to obtain the target miRNAs and the target genes. Next, we performed Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of the target genes. Then, we used Cytoscape 3.8.2 software to visualize and construct the circRNA-miRNA-mRNA regulatory network, the protein-protein interaction (PPI) network, and the autophagy-related genes network.\nRESULTS: We identified a total of 21 DECs, including 6 upregulated DECs and 15 downregulated DECs. After further analysis, we obtained a circRNA-miRNA-mRNA regulatory network consisting of 11 DECs, 9 target miRNAs and 410 target genes, and a PPI network. Finally, the potential novel genes of autophagy in AF were revealed by bioinformatics analysis.\nCONCLUSION: This study could explore the potential role of circRNA, autophagy-related genes and construct the circRNA-miRNA-mRNA regulation network in AF.", "claims": [{"id": "claim-method", "statement": "The DECs were analyzed by using the limma package in R software (version 4.1.0).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34848999", "locator": "sections[4] \"Identification of DECs\" paragraph 2", "quote": "The DECs were analyzed by using the limma package in R software (version 4.1.0)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE129409 dataset is available from the Gene Expression Omnibus GEO (http://www.ncbi.nlm.nih.gov/geo).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34848999", "locator": "sections[24] \"Data Sharing Statement\" paragraph 2", "quote": "The GSE129409 dataset is available from the Gene Expression Omnibus GEO (http://www.ncbi.nlm.nih.gov/geo)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 21 differentially expressed circRNAs were identified in atrial fibrillation, including 6 upregulated and 15 downregulated circRNAs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34848999", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified a total of 21 DECs, including 6 upregulated DECs and 15 downregulated DECs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 21 differentially expressed circRNAs were identified in atrial fibrillation, including 6 upregulated and 15 downregulated circRNAs.", "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:34848999"], "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:GSE129409"], "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:GSE129409"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34848999", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/IJGM.S333752", "sha256": "sha256:73df6055273d632063c3630b0fe7eee8fcf62426fd9f3f6192cb96498a0e33a4", "bytes": 33312, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/IJGM.S333752", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8612294", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE129409", "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=GSE129409", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE129409", "version": null, "note": "The GSE129409 dataset is available from the Gene Expression Omnibus GEO (http://www.ncbi.nlm.nih.gov/geo).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The GSE129409 dataset is available from the Gene Expression Omnibus GEO (http://www.ncbi.nlm.nih.gov/geo).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3712565", "GSM3712566", "GSM3712567", "GSM3712568", "GSM3712569", "GSM3712570"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "21825", "taxon": "Homo sapiens", "title": "The integrative regulatory network of circRNA, microRNA and mRNA in atrial fibrillation", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE129409 not downloaded", "asset:data:geo:GSE129409 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The DECs were analyzed by using the limma package in R software (version 4.1.0)."}}, {"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"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "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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