Differential expression profiles and functional analysis of long non-coding RNAs in calcific aortic valve disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37369992", "kind": "science-record", "revision": 4, "content_hash": "sha256:4d8a601962df227bcbb492da63099e344601b6c9f3d63f63216cf56df3d420b9", "created_at": "2026-11-01T19:02:06Z", "updated_at": "2026-11-01T22:52:11Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Differential expression profiles and functional analysis of long non-coding RNAs in calcific aortic valve disease.", "doi": "10.1186/s12872-023-03311-x", "pmid": "37369992", "authors": ["Guang-Yuan Song", "Xu-Nan Guo", "Jing Yao", "Zhi-Nan Lu", "Jia-Hong Xie", "Fang Wu", "Jing He", "Zhao-Lin Fu", "Jie Han"], "journal": "BMC cardiovascular disorders", "year": 2023, "abstract": "AIM: To evaluate the expression profile of long non-coding RNAs (lncRNAs) in calcific aortic valve disease (CAVD) and explore their potential mechanism of action.\nMETHODS: The gene expression profiles (GSE153555, GSE148219, GSE199718) were downloaded from the Gene Expression Omnibus (GEO) database and FastQC was run for quality control checks. After filtering and classifying candidate lncRNAs by differentially expressed genes (DEGs) and weighted co-expression networks (WGCNA) in GSE153555, we predicted the potential cis- or trans-regulatory target genes of differentially expressed lncRNAs (DELs) by using FEELnc and established the competitive endogenous RNA (ceRNA) network by miRanda, more over functional enrichment was analyzed using the ClusterProfiler package in R Bioconductor. The hub cis- or trans-regulatory genes were verified in GSE148219 and GSE199718 respectively.\nRESULTS: There were 340 up-regulated lncRNAs identified in AS group compared with the control group (|log2Fold Change| ≥ 1.0 and Padj ≤ 0.05), and 460 down-regulated lncRNAs. Based on target gene prediction and co-expression network construction, twelve Long non-coding RNAs (CDKN2B-AS1, AC244453.2, APCDD1L-DT, SLC12A5-AS1, TGFB3, AC243829.4, MIR4435-2HG, FAM225A, BHLHE40-AS1, LINC01614, AL356417.2, LINC01150) were identified as the hub cis- or trans-regulatory genes in the pathogenesis of CAVD which were validated in GSE148219 and GSE19971. Additionally, we found that MIR4435-2HG was the top hub trans-acting lncRNA which also plays a crucial role by ceRNA pattern.\nCONCLUSION: LncRNAs may play an important role in CAVD and may provide a new perspective on the pathogenesis, diagnosis, and treatment of this disease. Further studies are required to illuminate the underlying mechanisms and provide potential therapeutic targets.", "claims": [{"id": "claim-method", "statement": "Gene differential expression analysis was performed by DESeq2 v1.34.0 [25] in R/Bioconductor (R version 4.1.0).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37369992", "locator": "sections[13] \"Differential expression analysis of mRNAs and lncRNAs\" paragraph 2", "quote": "Gene differential expression analysis was performed by DESeq2 v1.34.0 [25] in R/Bioconductor (R version 4.1.0)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analysed during the current study are available in the NCBI-GEO database (https://www.ncbi.nlm.nih.gov/geo/). The data that support the findings of this study are available from the corresponding author, Guang-Yuan Song or Jie Han, upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37369992", "locator": "sections[25] \"Data Availability\" paragraph 2", "quote": "The datasets analysed during the current study are available in the NCBI-GEO database (https://www.ncbi.nlm.nih.gov/geo/). The data that support the findings of this study are available from the corresponding author, Guang-Yuan Song or Jie Han, upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Based on target gene prediction and co-expression network construction, twelve Long non-coding RNAs (CDKN2B-AS1, AC244453.2, APCDD1L-DT, SLC12A5-AS1, TGFB3, AC243829.4, MIR4435-2HG, FAM225A, BHLHE40-AS1, LINC01614, AL356417.2, LINC01150) were identified as the hub cis- or trans-regulatory genes in the pathogenesis of CAVD which were validated in GSE148219 and GSE19971.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37369992", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Based on target gene prediction and co-expression network construction, twelve Long non-coding RNAs (CDKN2B-AS1, AC244453.2, APCDD1L-DT, SLC12A5-AS1, TGFB3, AC243829.4, MIR4435-2HG, FAM225A, BHLHE40-AS1, LINC01614, AL356417.2, LINC01150) were identified as the hub cis- or trans-regulatory genes in the pathogenesis of CAVD which were validated in GSE148219 and GSE19971."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Based on target gene prediction and co-expression network construction, twelve Long non-coding RNAs (CDKN2B-AS1, AC244453.2, APCDD1L-DT, SLC12A5-AS1, TGFB3, AC243829.4, MIR4435-2HG, FAM225A, BHLHE40-AS1, LINC01614, AL356417.2, LINC01150) were identified as the hub cis- or trans-regulatory genes in the pathogenesis of CAVD which were validated in GSE148219 and GSE19971.", "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:37369992"], "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:GSE148219"], "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:GSE148219"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37369992", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12872-023-03311-x", "sha256": "sha256:f4e4bffe3b6bb12684de2aec6f6e359371fafc17023daf283a02905cc71ee5dc", "bytes": 42744, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12872-023-03311-x", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10294343", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE148219", "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=GSE148219", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE148219", "version": null, "note": "The datasets analysed during the current study are available in the NCBI-GEO database (https://www.ncbi.nlm.nih.gov/geo/). 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