The underlying molecular mechanisms and biomarkers of plaque vulnerability based on bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36303246", "kind": "science-record", "revision": 5, "content_hash": "sha256:45649c11355f875bd7c82e4a5497756aaf061c47e38033fc55fbfe3046a849d6", "created_at": "2026-11-01T18:15:43Z", "updated_at": "2026-11-01T22:50:29Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The underlying molecular mechanisms and biomarkers of plaque vulnerability based on bioinformatics analysis.", "doi": "10.1186/s40001-022-00840-7", "pmid": "36303246", "authors": ["Rui Cheng", "Xiaojiang Xu", "Shurong Yang", "Zhongqian Mi", "Yong Zhao", "Jinhua Gao", "Feiyan Yu", "Xiuyun Ren"], "journal": "European journal of medical research", "year": 2022, "abstract": "AIM: The study aimed to identify the underlying differentially expressed genes (DEGs) and mechanism of unstable atherosclerotic plaque using bioinformatics methods.\nMETHODS: GSE120521, which includes four unstable samples and four stable atherosclerotic samples, was downloaded from the GEO database. DEGs were identified using LIMMA. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs were performed using the Database for metascape Visualization online tool. Based on the STRING database, protein-protein interactions (PPIs) network among DEGs were constructed. Regulatory networks were visualized using Cytoscape. We use the xCell to analyze the different immune cell subtypes.\nRESULTS: A total of 1626 DEGs (1034 up-regulated and 592 down-regulated DEGs) were identified between unstable and stable samples. I pulled 62 transcription factors (34 up-regulated TFs and 28 down-regulated TFs) from the Trust database. The up-regulated TFs were mainly enrichment in positive regulation of myeloid leukocyte differentiation, and the down-regulated TFs were mainly enrichment in connective tissue development. In the PPI network, RB1, CEBPA, PPARG, BATF was the most significantly up-regulated gene in ruptured atherosclerotic samples. The immune cell composition enriched in CD cells and macrophages in the unstable carotid plaque.\nCONCLUSIONS: Upregulated RB1, CEBPA, PPARG, BATF and down-regulated SRF, MYOCD, HEY2, GATA6 might perform critical promotional roles in atherosclerotic plaque rupture, furthermore, number and polarization of macrophages may play an important role in vulnerable plaques.", "claims": [{"id": "claim-method", "statement": "After processed, DEGs between groups were screened out using the limma R package; p-value between gene expressions was determined using the T test and adjusted using Benjamini–Hochberg (BH) method.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36303246", "locator": "sections[5] \"Data preprocessing and identification of DEGs\" paragraph 2", "quote": "After processed, DEGs between groups were screened out using the limma R package; p-value between gene expressions was determined using the T test and adjusted using Benjamini–Hochberg (BH) method."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data generated or analyzed during this study are included in this published article.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36303246", "locator": "sections[23] \"Availability of data and materials\" paragraph 2", "quote": "All data generated or analyzed during this study are included in this published article."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 1626 DEGs (1034 up-regulated and 592 down-regulated DEGs) were identified between unstable and stable samples.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36303246", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 1626 DEGs (1034 up-regulated and 592 down-regulated DEGs) were identified between unstable and stable samples."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 1626 DEGs (1034 up-regulated and 592 down-regulated DEGs) were identified between unstable and stable samples.", "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:36303246"], "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:GSE120521"], "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:GSE120521"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36303246", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s40001-022-00840-7", "sha256": "sha256:0c88b1f54172b003abe1b1d18a870586b3d467e25255db233fc7897d92709c1a", "bytes": 30511, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s40001-022-00840-7", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9615401", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE120521", "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=GSE120521", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE120521", "version": null, "note": "All data generated or analyzed during this study are included in this published article.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "All data generated or analyzed during this study are included in this published article.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3402504", "GSM3402505", "GSM3402506", "GSM3402507", "GSM3402508", "GSM3402509", "GSM3402510", "GSM3402511"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "16791", "taxon": "Homo sapiens", "title": "RNA-seq of stable and unstable section of human atherosclerotic plaques", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE120521 not downloaded", "asset:data:geo:GSE120521 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": "After processed, DEGs between groups were screened out using the limma R package; 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