Differentially Expressed Genes and Their Clinical Significance in Ischaemic Stroke: An In-Silico Study.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33447134", "kind": "science-record", "revision": 5, "content_hash": "sha256:cb2ab2a8a6392ed95dbc9e8bbcb66c2f5e4d67ee8473bbd8bf4d417b87068506", "created_at": "2026-11-01T15:41:22Z", "updated_at": "2026-11-01T21:24:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Differentially Expressed Genes and Their Clinical Significance in Ischaemic Stroke: An In-Silico Study.", "doi": "10.21315/mjms2020.27.6.6", "pmid": "33447134", "authors": ["Sandeep Appunni", "Muni Rubens", "Venkataraghavan Ramamoorthy", "Hina Sharma", "Anjani Kumar Singh", "Vishnu Swarup", "Himanshu Narayan Singh"], "journal": "The Malaysian journal of medical sciences : MJMS", "year": 2020, "abstract": "BACKGROUND: Ischaemic stroke (IS), a multifactorial neurological disorder, is mediated by interplay between genes and the environment and, thus, blood-based IS biomarkers are of significant clinical value. Therefore, this study aimed to find global differentially expressed genes (DEGs) in-silico, to identify key enriched genes via gene set enrichment analysis (GSEA) and to determine the clinical significance of these genes in IS.\nMETHODS: Microarray expression dataset GSE22255 was retrieved from the Gene Expression Omnibus (GEO) database. It includes messenger ribonucleic acid (mRNA) expression data for the peripheral blood mononuclear cells of 20 controls and 20 IS patients. The bioconductor-package 'affy' was used to calculate expression and a pairwise t-test was applied to screen DEGs (P < 0.01). Further, GSEA was used to determine the enrichment of DEGs specific to gene ontology (GO) annotations.\nRESULTS: GSEA analysis revealed 21 genes to be significantly plausible gene markers, enriched in multiple pathways among all the DEGs (n = 881). Ten gene sets were found to be core enriched in specific GO annotations. JunD, NCX3 and fibroblast growth factor receptor 4 (FGFR4) were under-represented and glycoprotein M6-B (GPM6B) was persistently over-represented.\nCONCLUSION: The identified genes are either associated with the pathophysiology of IS or they affect post-IS neuronal regeneration, thereby influencing clinical outcome. These genes should, therefore, be evaluated for their utility as suitable markers for predicting IS in clinical scenarios.", "claims": [{"id": "claim-method", "statement": "GSEA results are based on the Kolmogorov-Smirnov (K-S) statistical test", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33447134", "locator": "sections[9] \"Functional Enrichment Analysis of Genomic Datasets in IS Using GSEA\" paragraph 7", "quote": "GSEA results are based on the Kolmogorov-Smirnov (K-S) statistical test"}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mRNA microarray expression dataset GSE22255, which is based on the Affymetrix Human Genome U133 Plus 2.0 Array (Affymetrix, Inc., Santa Clara, CA, USA), was retrieved from the Gene Expression Omnibus (GEO). This dataset includes mRNA expression data from the peripheral blood mononuclear cells of 20 controls and 20 IS patients.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33447134", "locator": "sections[3] \"Affymetrix Microarray Data\" paragraph 2", "quote": "The mRNA microarray expression dataset GSE22255, which is based on the Affymetrix Human Genome U133 Plus 2.0 Array (Affymetrix, Inc., Santa Clara, CA, USA), was retrieved from the Gene Expression Omnibus (GEO). This dataset includes mRNA expression data from the peripheral blood mononuclear cells of 20 controls and 20 IS patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:33447134"], "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:GSE22255"], "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:GSE22255"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33447134", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21315/mjms2020.27.6.6", "sha256": "sha256:18f281e6abb86547d1d7aee32b0dddeeb7be3c44c60e8c7412cb77d073c51c68", "bytes": 40091, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21315/mjms2020.27.6.6", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7785266", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE22255", "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=GSE22255", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE22255", "version": null, "note": "The mRNA microarray expression dataset GSE22255, which is based on the Affymetrix Human Genome U133 Plus 2.0 Array (Affymetrix, Inc., Santa Clara, CA, USA), was retrieved from the Gene Expression Omnibus (GEO). This dataset includes mRNA expression data from the peripheral blood mononuclear cells of 20 controls and 20 IS patients.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The mRNA microarray expression dataset GSE22255, which is based on the Affymetrix Human Genome U133 Plus 2.0 Array (Affymetrix, Inc., Santa Clara, CA, USA), was retrieved from the Gene Expression Omnibus (GEO). This dataset includes mRNA expression data from the peripheral blood mononuclear cells of 20 controls and 20 IS patients.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM554014", "GSM554015", "GSM554016", "GSM554017", "GSM554018", "GSM554019", "GSM554020", "GSM554021", "GSM554022", "GSM554023", "GSM554024", "GSM554025", "GSM554026", "GSM554027", "GSM554028", "GSM554029", "GSM554030", "GSM554031", "GSM554032", "GSM554033", "GSM554034", "GSM554035", "GSM554036", "GSM554037", "GSM554038", "GSM554039", "GSM554040", "GSM554041", "GSM554042", "GSM554043", "GSM554044", "GSM554045", "GSM554046", "GSM554047", "GSM554048", "GSM554049", "GSM554050", "GSM554051", "GSM554052", "GSM554053"], "sample_count": 40, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Blood genomic expression profile for ischemic stroke (IS)", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": 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