Identification of adriamycin resistance genes in breast cancer based on microarray data analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35117349", "kind": "science-record", "revision": 5, "content_hash": "sha256:810248f0ddbd6041441d855e368d0844911c911863d90788c847c4d3f37f4ab9", "created_at": "2026-11-01T17:36:51Z", "updated_at": "2026-11-01T22:05:46Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of adriamycin resistance genes in breast cancer based on microarray data analysis.", "doi": "10.21037/tcr-19-2145", "pmid": "35117349", "authors": ["Yan Chen", "Yingfeng Lin", "Zhaolei Cui"], "journal": "Translational cancer research", "year": 2020, "abstract": "BACKGROUND: Breast cancer is a common malignant tumor with increasing incidence worldwide. This study aimed to investigate the molecular mechanisms of the adriamycin (ADR) resistance in breast cancer.\nMETHODS: The GSE76540 dataset downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database was adopted for analysis. Differentially expressed genes (DEGs) in chemo-sensitive cases and chemo-resistant cases were identified using the GEO2R online tool respectively. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of DEGs were carried out by using the DAVID online tool. The protein-protein interaction (PPI) network was constructed using the Search Tool for the Retrieval of Interacting Genes (STRING) and visualized with Cytoscape software. The impact of key tumor genes on the survival and prognosis were described.\nRESULTS: A total of 1,481 DEGs were excavated, including 549 up-regulated genes and 932 down-regulated genes. According to the GO analysis, the DEGs were significantly enriched in: extracellular matrix organization, positive regulation of transcription from RNA polymerase II promoter, lung development, positive regulation of gene expression, axon guidance and so on. The results of KEGG pathway enrichment analysis showed that the most enriched DEGs can be detected in: pathways in cancer, PI3K/AKT signaling pathway, focal adhesion, Ras signaling pathway and so on. In the PPI network analysis, hub genes of CDH1, ESR1, SOX2, AR, GATA3, FOXA1, KRT19, CLDN7, AGR2, ESRP1, RAB25, CLDN4, IGF1R, CLDN3 and IRS1 were detected. Finally, there is a correlation filter out these hub genes in resistance of ADR.\nCONCLUSIONS: Hub genes associated with ADR resistance were identified using bioinformatic techniques. The results of this study may contribute to the development of targeted therapy for breast cancer.", "claims": [{"id": "claim-method", "statement": "The GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/, accessed January 25th, 2019) online tool was employed to detect the DEGs in chemo-sensitive cases and chemo-resistant cases (8), respectively. Adjusted P<0.01, P<0.01 and fold change (FC) ≥2 were considered as the cut-off criterion.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35117349", "locator": "sections[4] \"Screening for DEGs\" paragraph 2", "quote": "The GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/, accessed January 25th, 2019) online tool was employed to detect the DEGs in chemo-sensitive cases and chemo-resistant cases (8), respectively. Adjusted P<0.01, P<0.01 and fold change (FC) ≥2 were considered as the cut-off criterion."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The gene expression profile dataset was downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database (6) (http://www.ncbi.nlm.nih.gov/geo). The GSE76540 dataset (7) was based on the GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, consisting of 3 chemo-sensitive samples and 3 chemo-resistant samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35117349", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "The gene expression profile dataset was downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) database (6) (http://www.ncbi.nlm.nih.gov/geo). The GSE76540 dataset (7) was based on the GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array, consisting of 3 chemo-sensitive samples and 3 chemo-resistant samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 15 hub genes associated with adriamycin (ADR) resistance in breast cancer.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35117349", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "In the PPI network analysis, hub genes of CDH1, ESR1, SOX2, AR, GATA3, FOXA1, KRT19, CLDN7, AGR2, ESRP1, RAB25, CLDN4, IGF1R, CLDN3 and IRS1 were detected."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 15 hub genes associated with adriamycin (ADR) resistance in breast cancer.", "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:35117349"], "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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