Identification of Potential Breast Cancer Stem Cell Biomarkers in the Secretome Using a Network Interaction Approach Analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38809653", "kind": "science-record", "revision": 5, "content_hash": "sha256:0d00d4f07cec52f53fc0ebb341f096af8df22f3a12db41c49e8f41ade723d730", "created_at": "2026-11-01T19:20:46Z", "updated_at": "2026-11-01T22:54:24Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Potential Breast Cancer Stem Cell Biomarkers in the Secretome Using a Network Interaction Approach Analysis.", "doi": "10.31557/APJCP.2024.25.5.1803", "pmid": "38809653", "authors": ["Ay Ly Margaret", "Septelias Inawati Wanandi", "Fadilah Fadilah", "Rafika Indah Paramita"], "journal": "Asian Pacific journal of cancer prevention : APJCP", "year": 2024, "abstract": "BACKGROUND: Breast cancer stem cells (BCSCs) play a role in the high rates of resistance, recurrence, and metastasis. The precise biomarkers of BCSCs can assist effectively in identifying cancer, assessing prognosis, diagnosing, and monitoring therapy. The aim of this study was to give a complete analysis for predicting specific biomarkers of BCSCs.\nMETHODS: We aggregated profile datasets in this work to shed light on the underlying critical genes and pathways of BCSCs. We obtained two expression profiling by array datasets (GSE7513 and GSE7515) from the Gene Expression Omnibus (GEO) database to identify biomarkers in BCSCs. Enrichr was used to do functional analysis, including gene ontology (GO) and reactome pathway. Furthermore, the protein-protein interaction (PPI) of these differential expression genes (DEGs) was visualized using Cytoscape with the search tool for the retrieval of interacting genes (STRING). The hub genes in the PPI network were chosen for further investigation.\nRESULTS: We identified 65 up-regulated and 190 down- regulated DEGs and the GO enrichment analysis revealed that these DEGs were enriched in biological process related to tumorigenesis and stemness, including alter the extracellular matrix's physicochemical properties, cytoskeletal reorganisation, adhesion, motility, migration, growth, and survival. The Reactome analysis indicated that these DEGs were also involved in modulating function of ECM, regulation cancer metabolism and angiogenesis, tumor growth, proliferation, and metastasis.\nCONCLUSION: Our bioinformatic study revealed that FYN, INADL, OCLN, F11R, and TOP2A were potential biomarker panel of BCSCs from secretome.", "claims": [{"id": "claim-method", "statement": "GEO2R exploits the limma package to perform inter- and intra-sample normalization. We used the log data transformation approach to standardize the findings and the false discovery rate (FDR) p value correction for multiple testing in order to conduct DEG analysis.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38809653", "locator": "sections[2] \"Materials and Methods\" paragraph 4", "quote": "GEO2R exploits the limma package to perform inter- and intra-sample normalization. We used the log data transformation approach to standardize the findings and the false discovery rate (FDR) p value correction for multiple testing in order to conduct DEG analysis."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data supporting this study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38809653", "locator": "sections[5] \"ack\" paragraph 1", "quote": "The data supporting this study are available from the corresponding author upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "GEO2R analysis of GSE7513 and GSE7515 identified 258 common differentially expressed genes between breast cancer stem cells and non-breast cancer stem cells.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38809653", "locator": "sections[3] \"Results\" paragraph 3", "quote": "In the intersection of these two data sets, a total of 258 DEGs (65 upregulated and 193 downregulated genes) were identified and were visually represented in a Venn diagram (Figure 1B and 1C)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "GEO2R analysis of GSE7513 and GSE7515 identified 258 common differentially expressed genes between breast cancer stem cells and non-breast cancer stem cells.", "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:38809653"], "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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