Integrated Bioinformatics Data Analysis Reveals Prognostic Significance Of SIDT1 In Triple-Negative Breast Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31632087", "kind": "science-record", "revision": 8, "content_hash": "sha256:5b80e405a83a154bbd40507119f23ff586a8e73136829d69bb18eff504b3935a", "created_at": "2026-11-01T15:40:50Z", "updated_at": "2026-11-01T22:00:55Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated Bioinformatics Data Analysis Reveals Prognostic Significance Of SIDT1 In Triple-Negative Breast Cancer.", "doi": "10.2147/OTT.S215898", "pmid": "31632087", "authors": ["Ya Wang", "Hanning Li", "Jingjing Ma", "Tian Fang", "Xiaoting Li", "Jiahao Liu", "Henok Kessete Afewerky", "Xiong Li", "Qinglei Gao"], "journal": "OncoTargets and therapy", "year": 2019, "abstract": "BACKGROUND: Triple-negative breast cancer (TNBC) is a heterogeneous disease with a worse prognosis. However, current therapies have rarely improved the outcome of patients with TNBC. Here we sought to identify novel biomarkers or targets for TNBC.\nMATERIALS AND METHODS: Patients GSE76275 clinic traits and their corresponding mRNA profiles for 198 TNBC and 67 non-TNBC were obtained from the GEO database. Weighted gene co-expression network analysis (WGCNA) of the GSE76275 keyed out hub genes, and the differentially expressed genes (DEGs) were identified with the cut-off of adjusted P (adj. P) <0.01 and |log2 fold-change (FC)| > 1.5. The hub - DEGs overlapping genes, as key genes, were considered for further study using Kaplan-Meier plotter online analysis. Subsequently, Breast Cancer Gene-Expression Miner v4.0 and tissue microarray analysis were applied to determine the transcriptional and translational levels of every key gene. Following plasmid transfection for overexpression, the proliferation of TNBC cells was determined by CCK8 and colony formation assay. Moreover, xenograft tumor models were canvassed to investigate their effect upon in vivo tumor growth.\nRESULTS: Four genes (SIDT1, ANKRD30A, GPR160, and CA12) were found to be associated with relapse-free survival (RFS) in TNBC through WGCNA and DEGs integrated analysis. Patients with a higher level of SIDT1 had significantly better RFS compared to those with lower levels. The transcriptional and translational levels of SIDT1 were validated as downregulated in patients with triple-negative status, negative estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2). Furthermore, SIDT1 inhibited proliferation of breast cancer cells (MDA-MB-231 and MDA-MB-468) and xenograft studies demonstrated that SIDT1 can suppress tumor growth in vivo.\nCONCLUSION: This study suggests that SIDT1 may play a crucial role in TNBC progression and has the potential as a prognostic biomarker of TNBC.", "claims": [{"id": "claim-method", "statement": "Weighted gene co-expression network analysis (WGCNA) of the GSE76275 keyed out hub genes, and the differentially expressed genes (DEGs) were identified with the cut-off of adjusted P (adj. P) <0.01 and |log2 fold-change (FC)| > 1.5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31632087", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Weighted gene co-expression network analysis (WGCNA) of the GSE76275 keyed out hub genes, and the differentially expressed genes (DEGs) were identified with the cut-off of adjusted P (adj. P) <0.01 and |log2 fold-change (FC)| > 1.5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The mRNA expression profiles and corresponding patient clinic traits were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) with accession number GSE76275.12 In total, 265 samples (198 TNBC and 67 non-TNBC) analyzed on the Affymetrix Human Genome U133 Plus 2.0 Array platforms were included in the dataset.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31632087", "locator": "sections[9] \"Data Collection And Preprocessing\" paragraph 2", "quote": "The mRNA expression profiles and corresponding patient clinic traits were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/) with accession number GSE76275.12 In total, 265 samples (198 TNBC and 67 non-TNBC) analyzed on the Affymetrix Human Genome U133 Plus 2.0 Array platforms were included in the dataset."}], "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:31632087"], "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:GSE76275"], "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:GSE76275"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31632087", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/OTT.S215898", "sha256": 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(A) IHC analysis of SIDT1 protein in human"], "order_basis": "paper_text_order:902", "id": "assay:1"}, {"role": "data_generation", "definition_id": "transfection", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["levels of every key gene. Following plasmid transfection for overexpression, the proliferation of TNB", "Materials And Methods Cell Culture And Transfection Human breast cancer lines MDA-MB-231 and MDA", "ions were performed using X-tremeGENE HP DNA Transfection Reagent (Cat. #739406, Roche) following the"], "order_basis": "paper_text_order:1031", "id": "assay:2"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["roliferation of TNBC cells was determined by CCK8 and colony formation assay. Moreover, xenogr"], "order_basis": "paper_text_order:1113", "id": "assay:3"}, {"role": "data_generation", "definition_id": "animal_model", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["e canvassed to investigate their effect upon in vivo tumor growth. RESULTS: Four genes (SIDT1, AN", "strated that SIDT1 can suppress tumor growth in vivo. CONCLUSION: This study suggests that SIDT1", "Four-week-old 24 female athymic nude (nu/nu) mice were purchased from HFK Bio-Technology Co. Ltd. (", "subcutaneously into the caudal thigh of each mouse. Tumor volumes were calculated every 7 days"], "order_basis": "paper_text_order:1227", "id": "assay:4"}, {"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["and MDA-MB-468 were purchased from ATCC and cultured in DMEM medium with 10% fetal bovine serum (FBS"], "order_basis": "paper_text_order:2216", "id": "assay:5"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["fy the expression of SIDT1 in breast cancer, immunohistochemical analysis was conducted in tissue samples. As", "cancer patients using tissue microarray. (A) IHC analysis of SIDT1 protein in human breast sp", "resentative images of SIDT1 staining and the IHC scores (Hscore) are shown. Enlarged local im"], "order_basis": "paper_text_order:4895", "id": "assay:6"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["ANOVA"], "order_basis": "consumes_earlier_output", "id": "assay:7"}]}