Transcriptomic analyses identify key differentially expressed genes and clinical outcomes between triple-negative and non-triple-negative breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30613165", "kind": "science-record", "revision": 7, "content_hash": "sha256:a9c01a505b26fd1cf969ef0225e8ec0e32683a299eafa7609512a2cff5583110", "created_at": "2026-11-01T15:40:40Z", "updated_at": "2026-11-01T21:21:51Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Transcriptomic analyses identify key differentially expressed genes and clinical outcomes between triple-negative and non-triple-negative breast cancer.", "doi": "10.2147/CMAR.S187151", "pmid": "30613165", "authors": ["Bo Chen", "Hailin Tang", "Xi Chen", "Guochun Zhang", "Yulei Wang", "Xiaoming Xie", "Ning Liao"], "journal": "Cancer management and research", "year": 2019, "abstract": "PURPOSE: There are significant differences in the biological behavior between triple-negative breast cancer (TNBC) and non-triple-negative breast cancer (non-TNBC). In the present study, we identify key differential genes and clinical outcomes between TNBC and non-TNBC.\nMATERIALS AND METHODS: Transcriptomic analyses used GEO datasets (GSE76275), gene ontology, KEGG pathway analysis and cBioPortal. Quantitative RT-PCR analysis (qRT-PCR) was used to validate the differentially expressed genes. We used the KM Plotter Online Tool and 240 patients with TNBC tissue microarray to assay the prognostic value of HORMAD1.\nRESULTS: The upregulated differentially expressed genes were enriched in transcription factor activity, sequence-specific DNA binding and nucleic acid binding transcription factor activity. Only 16 genes were upregulated when further screened for fold change >4-fold change. HORMAD1 and SOX8 exhibited high frequencies of change of greater than 10% (HORMAD1 was close to 20%). qRT-PCR results indicated that HORMAD1 and SOX8 mRNA levels were significantly upregulated in TNBC samples. In KM Plotter Online Tool, high HORMAD1 was associated with worse outcome. In our tissue microarray (including 240 TNBC tissues), IHC analysis revealed that 29.7% (55/240) of the tumor samples exhibited high HORMAD1 expression and 70.3% (185/240) of the tumor samples exhibited low HORMAD1 expression levels. Meanwhile, high HORMAD1 group has a bad prognosis.\nCONCLUSION: The status of transcriptional activation is an important difference between TNBC and non-TNBC. HORMAD1 is a key differential gene associated with poor outcome in TNBC. Epigenetic therapy and agents targeting cancer/testis antigens might potentially help to customize therapies of TNBC.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes were analyzed by GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30613165", "locator": "sections[3] \"Microarray data\" paragraph 2", "quote": "Differentially expressed genes were analyzed by GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We extracted gene expression profiles of TNBC and non-TNBC from a GEO database (GSE76275) that contained 265 samples, including 198 TNBC samples and 67 non-TNBC samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30613165", "locator": "sections[3] \"Microarray data\" paragraph 2", "quote": "We extracted gene expression profiles of TNBC and non-TNBC from a GEO database (GSE76275) that contained 265 samples, including 198 TNBC samples and 67 non-TNBC samples."}], "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:30613165"], "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:30613165", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/CMAR.S187151", "sha256": "sha256:8e8df16703f47c9e8e49bdfd501ed0573b71c348ad72cf2775920523a570acac", "bytes": 32959, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2147/CMAR.S187151", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6306052", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE76275", "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=GSE76275", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE76275", "version": null, "note": "We extracted gene expression profiles of TNBC and non-TNBC from a GEO database (GSE76275) that contained 265 samples, including 198 TNBC 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"bytes": 1658, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[13]/table-wrap[1]#t2-cmar-11-179", "version": null, "note": "The 16 upregulation identified genes", "structure": {"pmcid": "PMC6306052", "section_index": 13, "section_title": "HORMAD1 and SOX8 are key differential genes that are upregulated in TNBC", "row_count": 20, "column_count": 6}, "table": {"label": "Table 2", "caption": "The 16 upregulation identified genes", "rows": [["Gene symbol", "Gene name", "Probe set", "Log2 FC", "P-value", "Adj. P-value"], [""], ["PROM1", "Prominin 1", "204304_s_at", "2.87", "5.67E-16", "1.27E-14"], ["GABRP", "Gamma-aminobutyric acid type A receptor pi subunit", "205044_at", "2.86", "1.79E-13", "2.71E-12"], ["FABP7", "Fatty acid binding protein 7", "205030_at", "2.82", "1.91E-11", "2.06E-10"], ["", "", "205029_s_at", "2.09", "5.40E-11", "5.40E-10"], ["ROPN1", "Rhophilin associated tail protein 1", "231535_x_at", "2.71", "3.17E-22", "1.63E-20"], ["VGLL1", "Vestigial like family member 1", "215729_s_at", "2.64", "1.18E-17", "3.36E-16"], ["SHC4", "SHC adaptor protein 4", "235238_at", "2.54", "2.87E-19", "1.01E-17"], ["", "", "230538_at", "2.04", "8.23E-22", "4.00E-20"], ["HORMAD1", "HORMA domain containing 1", "223861_at", "2.51", "1.55E-18", "4.93E-17"], ["FOXC1", "Forkhead box C1", "1553613_s_at", "2.47", "4.22E-23", "2.42E-21"], ["EN1", "Engrailed homeobox 1", "220559_at", "2.46", "2.10E-29", "2.39E-27"], ["PSAT1", "Phosphoserine aminotransferase 1", "223062_s_at", "2.45", "8.26E-18", 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