Dataset for proteomic analysis of arylamine N-acetyltransferase 1 knockout MDA-MB-231 breast cancer cells.

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An unbiased analysis of proteomes of parental MDA-MB-231 breast cancer cells and two separate NAT1 knockout (KO) cell lines were performed. Among 4,890 proteins identified, 737 and 651 proteins were found significantly (p < 0.01) upregulated and downregulated, respectively, in NAT1 KO cells, compared to the parental cells. Each set of proteins was analyzed to identify Gene Ontology biological processes, molecular functions, and cellular components that were enriched in the set. Among the proteins upregulated in NAT1 KO cells, processes associated with MHC major histocompatibility complex I-mediated antigen presentation were significantly enriched. Multiple processes involved in mitochondrial functions were collectively downregulated in NAT1 KO cells, including multiple subunits of mitochondrial ATP synthase (Complex V of the electron transport chain). This was accompanied by a reduction in cell cycle-associated proteins and an increase in pro-apoptotic pathways in NAT1 KO cells. The current dataset contains additional representations of the biological processes and components that are differentially enriched in NAT1 KO MDA-MB-231 cells and will serve as a basis for generating novel hypotheses regarding the role of NAT1 in breast cancer. Data are available via ProteomeXchange with identifier PXD035953.", "claims": [{"id": "claim-method", "statement": "Gene Ontology (GO) biological processes, molecular functions, and cellular components that are significantly enriched (q [FDR] < 0.01) among proteins upregulated or downregulated in NAT1 KO cells were identified using GOnet [1] and PANTHER Overrepresentation Test [2].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36426076", "locator": "sections[3] \"Data Description\" paragraph 3", "quote": "Gene Ontology (GO) biological processes, molecular functions, and cellular components that are significantly enriched (q [FDR] < 0.01) among proteins upregulated or downregulated in NAT1 KO cells were identified using GOnet [1] and PANTHER Overrepresentation Test [2]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Proteomic Analysis of Arylamine N-Acetyltransferase 1 Knockout Breast Cancer Cells (Original data) (ProteomeXchange via the PRIDE database).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36426076", "locator": "sections[12] \"Data Availability\" paragraph 2", "quote": "Proteomic Analysis of Arylamine N-Acetyltransferase 1 Knockout Breast Cancer Cells (Original data) (ProteomeXchange via the PRIDE database)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Among 4,890 proteins identified, 737 and 651 proteins were found significantly (p < 0.01) upregulated and downregulated, respectively, in NAT1 KO cells, compared to the parental cells.", "kind": "quantitative", "target": {"value": 0.01, "unit": "p-value", "tolerance": null, "source": "Among 4,890 proteins identified, 737 and 651 proteins were found significantly (p < 0.01) upregulated and downregulated, respectively, in NAT1 KO cells, compared to the parental cells."}, "evidence": [{"asset": "source:pmid:36426076", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Among 4,890 proteins identified, 737 and 651 proteins were found significantly (p < 0.01) upregulated and downregulated, respectively, in NAT1 KO cells, compared to the parental cells."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Among 4,890 proteins identified, 737 and 651 proteins were found significantly (p < 0.01) upregulated and downregulated, respectively, in NAT1 KO cells, compared to the parental 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:36426076"], "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": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. 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