FAM201A, a long noncoding RNA potentially associated with atrial fibrillation identified by ceRNA network analyses and WGCNA.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35410298", "kind": "science-record", "revision": 5, "content_hash": "sha256:1652ed177d0965442dbbeeac8aa16e17d71941cdfc08bcbe722e859b27b35d45", "created_at": "2026-11-01T18:14:13Z", "updated_at": "2026-11-01T22:48:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "FAM201A, a long noncoding RNA potentially associated with atrial fibrillation identified by ceRNA network analyses and WGCNA.", "doi": "10.1186/s12920-022-01232-w", "pmid": "35410298", "authors": ["Xi Chen", "Xiang-Yu He", "Qing Dan", "Yang Li"], "journal": "BMC medical genomics", "year": 2022, "abstract": "BACKGROUND: Being the most common arrhythmia in clinic, atrial fibrillation (AF) causes various comorbidities to patients such as heart failure and stroke. LncRNAs were reported involved in pathogenesis of AF, yet, little is known about AF-associated lncRNAs. The present study aims to explore lncRNAs associated with AF susceptibility based on competing endogenous RNA (ceRNA) network analysis and weighted gene co-expression network analysis (WGCNA).\nMETHODS: GSE41177 and GSE79768 datasets were obtained from the Gene Expression Omnibus (GEO) database. Competing endogenous RNA (ceRNA) network analysis was performed using GSE41177. Differentially expressed lncRNAs (DElncRNAs), mRNAs (DEmRNAs) between AF patients and patients with sinus rhythm (SR) were identified from GSE41177 using R software. Then, the ceRNA network was constructed based on DElncRNAs, the predicted target miRNAs and DEmRNAs. Weighted gene co-expression network analysis (WGCNA) was performed using GSE79768 to validate the AF-related lncRNAs identified from GSE41177. LncRNA modules and crucial lncRNAs relevant to AF and were identified.\nRESULTS: In summary, 18 DElncRNAs and 350 DEmRNAs were found between AF patients and SR patients. A total of 5 lncRNAs, 10 miRNAs, and 21 mRNAs were contained in the final ceRNA network. Taking into consideration both the ceRNA theory and inference scores from the comparative toxicogenomics database (CTD) database, the ceRNA axis FAM201A-miR-33a-3p-RAC3 was identified as mostly relevant to AF susceptibility. FAM201A (Gene significance, GS = - 0.62; Module membership, MM = 0.75) was also proved in the blue module, which was identified most highly relevant with AF by WGCNA.\nCONCLUSIONS: These results demonstrated that decreased expression of FAM201A might be associated with susceptibility of AF. Working as the ceRNA to regulate RAC3 might be one function of FAM201A in AF susceptibility, which requires further exploration in future research.", "claims": [{"id": "claim-method", "statement": "Identification of differentially expressed lncRNAs (DElncRNAs), mRNAs (DEmRNAs) between AF patients and SR patients were performed using the “limma” package of R software (Version 3.6.3) [24].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35410298", "locator": "sections[4] \"Differential lncRNA and mRNA expression analyses\" paragraph 2", "quote": "Identification of differentially expressed lncRNAs (DElncRNAs), mRNAs (DEmRNAs) between AF patients and SR patients were performed using the “limma” package of R software (Version 3.6.3) [24]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets (accession number: GSE41177; accession number: GSE79768) used in the present study are available in the GEO database. The dataset GSE41177 can be accessed in the website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41177. The dataset GSE79768 can be accessed in the website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79768.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35410298", "locator": "sections[23] \"Availability of data and materials\" paragraph 2", "quote": "The datasets (accession number: GSE41177; accession number: GSE79768) used in the present study are available in the GEO database. The dataset GSE41177 can be accessed in the website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41177. The dataset GSE79768 can be accessed in the website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79768."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Taking into consideration both the ceRNA theory and inference scores from the comparative toxicogenomics database (CTD) database, the ceRNA axis FAM201A-miR-33a-3p-RAC3 was identified as mostly relevant to AF susceptibility.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35410298", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Taking into consideration both the ceRNA theory and inference scores from the comparative toxicogenomics database (CTD) database, the ceRNA axis FAM201A-miR-33a-3p-RAC3 was identified as mostly relevant to AF susceptibility."}, {"asset": "source:pmid:35410298", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "FAM201A (Gene significance, GS = − 0.62; Module membership, MM = 0.75) was also proved in the blue module, which was identified most highly relevant with AF by WGCNA."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Taking into consideration both the ceRNA theory and inference scores from the comparative toxicogenomics database (CTD) database, the ceRNA axis FAM201A-miR-33a-3p-RAC3 was identified as mostly relevant to AF susceptibility.", "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:35410298"], "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:GSE41177"], "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:GSE41177"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35410298", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12920-022-01232-w", "sha256": "sha256:a62b55938189c58ef645a6ec3253fd90a7ed2dba8306f21476d2cab7d0d52402", "bytes": 40512, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12920-022-01232-w", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8996407", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE41177", "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=GSE41177", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE41177", "version": null, "note": "The datasets (accession number: GSE41177; accession number: GSE79768) used in the present study are available in the GEO database. The dataset GSE41177 can be accessed in the website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41177. The dataset GSE79768 can be accessed in the website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79768.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets (accession number: GSE41177; accession number: GSE79768) used in the present study are available in the GEO database. The dataset GSE41177 can be accessed in the website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41177. The dataset GSE79768 can be accessed in the website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79768.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1005418", "GSM1005419", "GSM1005420", "GSM1005421", "GSM1005422", "GSM1005423", "GSM1005424", "GSM1005425", "GSM1005426", "GSM1005427", "GSM1005428", "GSM1005429", "GSM1005430", "GSM1005431", "GSM1005432", "GSM1005433", "GSM1005434", "GSM1005435", "GSM1005436", "GSM1005437", "GSM1005438", "GSM1005439", "GSM1005440", "GSM1005441", "GSM1005442", "GSM1005443", "GSM1005444", "GSM1005445", "GSM1006245", "GSM1006246", "GSM1006247", "GSM1006248", "GSM1006249", "GSM1006250", "GSM1006251", "GSM1006252", "GSM1006253", "GSM1006254"], "sample_count": 38, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Region-specific gene expression profiles in left atria of patients with valvular atrial fibrillation", "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:GSE79768", "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=GSE79768", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE79768", "version": null, "note": "The datasets (accession number: GSE41177; accession number: GSE79768) used in the present study are available in the GEO database. The dataset GSE41177 can be accessed in the website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41177. The dataset GSE79768 can be accessed in the website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79768.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets (accession number: GSE41177; accession number: GSE79768) used in the present study are available in the GEO database. The dataset GSE41177 can be accessed in the website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41177. The dataset GSE79768 can be accessed in the website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79768.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2102184", "GSM2102185", "GSM2102186", "GSM2102187", "GSM2102188", "GSM2102189", "GSM2102190", "GSM2102191", "GSM2102192", "GSM2102193", "GSM2102194", "GSM2102195", "GSM2102196", "GSM2102197", "GSM2102198", "GSM2102199", "GSM2102200", "GSM2102201", "GSM2102202", "GSM2102203", "GSM2102204", "GSM2102205", "GSM2102206", "GSM2102207", "GSM2102208", "GSM2102209"], "sample_count": 26, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Atrial fibrillation is associated with altered left-to-right atria gene expression ratio: implications for arrhythmogenesis and thrombogenesis", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE41177 not downloaded", "asset:data:geo:GSE41177 licence not read", "asset:data:geo:GSE79768 not downloaded", "asset:data:geo:GSE79768 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": "Identification of differentially expressed lncRNAs (DElncRNAs), mRNAs (DEmRNAs) between AF patients and SR patients were performed using the “limma” package of R software (Version 3.6.3) [24]."}}, {"id": "method-2", "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": 0.8, "band": "high", "quote": "GO 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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE41177", "GSE79768"], "resolved_accessions": ["GSE41177", "GSE79768"], "statements": ["The datasets (accession number: GSE41177; accession number: GSE79768) used in the present study are available in the GEO database. The dataset GSE41177 can be accessed in the website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE41177. The dataset GSE79768 can be accessed in the website: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE79768."], "basis": "The paper names GSE41177, GSE79768 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:35410298", "data:geo:GSE41177"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE41177"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:41:24Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12553, "completion_tokens": 2260, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:35410298", "type": "paper", "label": "pmid:35410298"}, {"id": "source:pmid:35410298", "type": "manuscript", "label": "PMID 35410298 full text"}, {"id": "data:geo:GSE41177", "type": "dataset", "label": "GEO GSE41177"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35410298", "type": "paper", "label": "pmid:35410298"}, {"id": "source:pmid:35410298", "type": "manuscript", "label": "PMID 35410298 full text"}, {"id": "data:geo:GSE41177", "type": "dataset", "label": "GEO GSE41177"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35410298", "type": "extraction", "used": ["source:pmid:35410298"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE41177", "type": "accession_resolution", "used": ["data:geo:GSE41177"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:35410298", "parent_hash": "sha256:990ba587ffe4d4c4ad7c36fd3ce92378afc75f5e1ff035855eee807d45573c22", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE41177 licence not read", "asset:data:geo:GSE41177 not downloaded", "asset:data:geo:GSE79768 licence not read", "asset:data:geo:GSE79768 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Identification of differentially expressed lncRNAs (DElncRNAs), mRNAs (DEmRNAs) between AF patients and SR patients were performed using the “limma” package of R software (Version 3.6.3) [24]."], "order_basis": "analysis_only", "id": "assay:1"}]}