Identification of Potential Key Genes and Pathways for Inflammatory Breast Cancer Based on GEO and TCGA Databases.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32606769", "kind": "science-record", "revision": 9, "content_hash": "sha256:33179e0209fd326c454e8c969ae94062237ef9a4f0adf1573d3562f474c6dae8", "created_at": "2026-11-01T15:41:05Z", "updated_at": "2026-11-01T22:45:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Potential Key Genes and Pathways for Inflammatory Breast Cancer Based on GEO and TCGA Databases.", "doi": "10.2147/OTT.S255300", "pmid": "32606769", "authors": ["Qing Lv", "Yansong Liu", "Hu Huang", "Mingjie Zhu", "Junqiang Wu", "Dong Meng"], "journal": "OncoTargets and therapy", "year": 2020, "abstract": "INTRODUCTION: Inflammatory breast cancer (IBC) is a rare type of breast cancer with poor prognosis, and the pathogenesis of this life-threatening disease is yet to be fully elucidated. This study aims to identify key genes of IBC, which could be potential diagnostic or therapeutic targets.\nMETHODS: Four datasets GSE5847, GSE22597, GSE23720, and GSE45581 were downloaded from the Gene Expression Omnibus (GEO) and differential expression analysis was performed. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted to understand the potential bio-functions of the differentially expressed genes (DEGs). Protein-protein interaction (PPI) network was constructed for functional modules analysis and hub genes identification, and TCGA survival analysis and qRT-PCR of clinical samples were used to further explore and validate the effect of hub genes on IBC.\nRESULTS: A total of 114 DEGs were identified from the GEO datasets. GO and KEGG analyses showed that the DEGs were mainly enriched in oncogenesis and cell adhesion. From the PPI network, we screened out five hub genes, including PTPRC, IL6, SELL, CD40, and SPN. Survival analysis and expression validation verified the robustness of the hub genes.\nDISCUSSION: The present study provides new insight into the understanding of IBC pathogenesis and the identified hub genes may serve as potential targets for diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "The R package, limma (https://www.bioconductor.org/packages/release/bioc/html/limma.html), was applied to analyze differential expression. Bayes tests were used to evaluate statistical significance.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32606769", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The R package, limma (https://www.bioconductor.org/packages/release/bioc/html/limma.html), was applied to analyze differential expression. Bayes tests were used to evaluate statistical significance."}], "state": "complete"}, {"id": "claim-data-access", "statement": "To identify genes differentially expressed in IBC and non-IBC tissues, microarray datasets (GSE5847,9 GSE22597,10 GSE23720,11 and GSE4558112) were downloaded from Genome Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo) database, and probe names in each expression matrix were annotated to Entrez ID according to the corresponding GEO platform files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32606769", "locator": "sections[3] \"Microarray Dataset Selection and Processing\" paragraph 2", "quote": "To identify genes differentially expressed in IBC and non-IBC tissues, microarray datasets (GSE5847,9 GSE22597,10 GSE23720,11 and GSE4558112) were downloaded from Genome Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo) database, and probe names in each expression matrix were annotated to Entrez ID according to the corresponding GEO platform files."}], "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:32606769"], "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. 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