Multi-omics data integration reveals correlated regulatory features of triple negative breast cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34142686", "kind": "science-record", "revision": 3, "content_hash": "sha256:cd0aa609379ac8ca074f280e3886681410ac7052c5c3d1964a56eb95a51d8630", "created_at": "2026-11-01T17:35:29Z", "updated_at": "2026-11-01T21:25:33Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Multi-omics data integration reveals correlated regulatory features of triple negative breast cancer.", "doi": "10.1039/d1mo00117e", "pmid": "34142686", "authors": ["Kevin Chappell", "Kanishka Manna", "Charity L Washam", "Stefan Graw", "Duah Alkam", "Matthew D Thompson", "Maroof Khan Zafar", "Lindsey Hazeslip", "Christopher Randolph", "Allen Gies", "Jordan T Bird", "Alicia K Byrd", "Sayem Miah", "Stephanie D Byrum"], "journal": "Molecular omics", "year": 2021, "abstract": "Triple negative breast cancer (TNBC) is an aggressive type of breast cancer with very little treatment options. TNBC is very heterogeneous with large alterations in the genomic, transcriptomic, and proteomic landscapes leading to various subtypes with differing responses to therapeutic treatments. We applied a multi-omics data integration method to evaluate the correlation of important regulatory features in TNBC BRCA1 wild-type MDA-MB-231 and TNBC BRCA1 5382insC mutated HCC1937 cells compared with non-tumorigenic epithelial breast MCF10A cells. The data includes DNA methylation, RNAseq, protein, phosphoproteomics, and histone post-translational modification. Data integration methods identified regulatory features from each omics method that had greater than 80% positive correlation within each TNBC subtype. Key regulatory features at each omics level were identified distinguishing the three cell lines and were involved in important cancer related pathways such as TGFβ signaling, PI3K/AKT/mTOR, and Wnt/beta-catenin signaling. We observed overexpression of PTEN, which antagonizes the PI3K/AKT/mTOR pathway, and MYC, which downregulates the same pathway in the HCC1937 cells relative to the MDA-MB-231 cells. The PI3K/AKT/mTOR and Wnt/beta-catenin pathways are both downregulated in HCC1937 cells relative to MDA-MB-231 cells, which likely explains the divergent sensitivities of these cell lines to inhibitors of downstream signaling pathways. The DNA methylation and RNAseq data is freely available via GEO GSE171958 and the proteomics data is available via the ProteomeXchange PXD025238.", "claims": [{"id": "claim-method", "statement": "We used the Data Integration Analysis for Biomarker discovery (DIABLO) with the sparse partial least squares regression (sPLS) method with tuning parameter set to keep the top 15 and 10 features for each data set corresponding to principal component 1 and 2, respectively.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34142686", "locator": "sections[9] \"Data integration\" paragraph 4", "quote": "We used the Data Integration Analysis for Biomarker discovery (DIABLO) with the sparse partial least squares regression (sPLS) method with tuning parameter set to keep the top 15 and 10 features for each data set corresponding to principal component 1 and 2, respectively."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The DNA methylation and RNAseq data is freely available via GEO GSE171958 and the proteomics data is available via the ProteomeXchange PXD025238.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34142686", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The DNA methylation and RNAseq data is freely available via GEO GSE171958 and the proteomics data is available via the ProteomeXchange PXD025238."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Data integration methods identified regulatory features from each omics method that had greater than 80% positive correlation within each TNBC subtype.", "kind": "quantitative", "target": {"value": 80.0, "unit": "per cent", "tolerance": null, "source": "Data integration methods identified regulatory features from each omics method that had greater than 80% positive correlation within each TNBC subtype."}, "evidence": [{"asset": "source:pmid:34142686", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Data integration methods identified regulatory features from each omics method that had greater than 80% positive correlation within each TNBC subtype."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Data integration methods identified regulatory features from each omics method that had greater than 80% positive correlation within each TNBC subtype.", "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:34142686"], "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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