Bioinformatics Analysis of Key Genes and Pathways Associated with Thrombosis in Essential Thrombocythemia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31801935", "kind": "science-record", "revision": 5, "content_hash": "sha256:8089b72f36a711da1c0f26abba7a80891029c9366161a6b5412336b5c8f21c84", "created_at": "2026-11-01T15:40:52Z", "updated_at": "2026-11-01T22:01:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis of Key Genes and Pathways Associated with Thrombosis in Essential Thrombocythemia.", "doi": "10.12659/MSM.918719", "pmid": "31801935", "authors": ["Chao Guo", "Zhenling Li"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2019, "abstract": "BACKGROUND Essential thrombocythemia (ET) is a form of chronic myeloproliferative neoplasm (MPN), and thrombosis is an important complication. This study aimed to use bioinformatics analysis to identify differentially expressed genes (DEGs) in ET associated thrombosis. MATERIAL AND METHODS Two datasets were identified from the Gene Expression Omnibus (GEO) database to investigate the expression profiles in ET. The GSE103176 dataset included 24 patients with ET and 15 healthy individuals with samples from CD34+ bone marrow cells. The GSE54644 dataset included 47 patients with ET and 11 healthy individuals with samples from peripheral neutrophils. GEO2R was used to screen DEGs, followed by over-representation analysis. Protein-protein interaction (PPI) network analysis and module analysis were performed using the STRING database and Cytoscape software. Hub genes were identified using the cytoHubba Cytoscape plugin, and maximal clique centrality (MCC) was identified. The MCODE Cytoscape plugin was used to identify network clusters, or highly interconnected regions. RESULTS There were 586 and 392 DEGs identified from the GSE103176 and GSE54644 datasets, respectively. The upregulated DEGs for CD34+ cells were predominantly enriched for granulocyte activation or related pathways for biological process (BP), and secretory vesicle for the cellular component (CC). The top hub genes within CD34+ cells included CXCL1, CAMP, HP, MMP8, PTX3, ORM1, LYZ, LTF, PGLYRP1, and OLFM4. CONCLUSIONS Bioinformatics analysis identified DEGs and hub genes that interacted with CD34+ cells and neutrophils that may predict an increased risk of thrombosis in patients with ET. These preliminary findings should be validated using next-generation sequencing (NGS) and clinical studies.", "claims": [{"id": "claim-method", "statement": "The GEO2R tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) was used to distinguish DEG in ET by comparison with healthy controls. An adjusted p-value <0.01 and |log2FC| >1 were defined as the criteria for DEG.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31801935", "locator": "sections[4] \"Identification of differentially expressed genes (DEGs) in essential thrombocythemia (ET)\" paragraph 2", "quote": "The GEO2R tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/) was used to distinguish DEG in ET by comparison with healthy controls. An adjusted p-value <0.01 and |log2FC| >1 were defined as the criteria for DEG."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The GSE103176 dataset was obtained from the GPL13667 platform (HG-U219) Affymetrix Human Genome U219 Array, and the GSE54644 was obtained from the GPL4685 platform (U133AAofAv2) Affymetrix GeneChip HT-HG_U133A Early Access Array. GEO103176 included expression profiles of bone marrow CD34+ cells from 24 ET and 15 healthy individuals.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31801935", "locator": "sections[3] \"Data source\" paragraph 2", "quote": "The GSE103176 dataset was obtained from the GPL13667 platform (HG-U219) Affymetrix Human Genome U219 Array, and the GSE54644 was obtained from the GPL4685 platform (U133AAofAv2) Affymetrix GeneChip HT-HG_U133A Early Access Array. GEO103176 included expression profiles of bone marrow CD34+ cells from 24 ET and 15 healthy individuals."}], "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:31801935"], "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:GSE103176"], "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:GSE103176"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31801935", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.918719", "sha256": "sha256:dc5989ab64586ea9bcc1f193b4bde76b83d7f881c25d87d0a4243c37232297d0", "bytes": 21102, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12659/MSM.918719", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6911306", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE103176", "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=GSE103176", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE103176", "version": null, "note": "The GSE103176 dataset was obtained from the GPL13667 platform (HG-U219) Affymetrix Human Genome U219 Array, and the GSE54644 was obtained from the GPL4685 platform (U133AAofAv2) Affymetrix GeneChip HT-HG_U133A Early Access Array. 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