Proteome-wide dataset supporting functional study of tyrosine kinases in breast cancer.

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Through a combined use of RNAi and stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative proteomics, a global functional proteomic landscape of TKs in breast cancer was recently revealed highlighting a comprehensive and highly integrated signaling network regulated by TKs (Stebbing et al., 2015) [1]. We collate the enormous amount of the proteomic data in an open access platform, providing a valuable resource for studying the function of TKs in cancer and benefiting the science community. Here we present a detailed description related to this study (Stebbing et al., 2015) [1] and the raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the identifier PXD002065.", "claims": [{"id": "claim-method", "statement": "Significance B test was used to characterize the most significantly regulated proteins after silencing of TKs (p<0.05) [8].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27054188", "locator": "sections[11] \"Bioinformatics analysis\" paragraph 2", "quote": "Significance B test was used to characterize the most significantly regulated proteins after silencing of TKs (p<0.05) [8]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the identifier PXD002065.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27054188", "locator": "sections[2] \"table-wrap\" paragraph 1", "quote": "The raw data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the identifier PXD002065."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The paper used the Significance B test (p<0.05) to identify significantly regulated proteins, and the raw mass-spectrometry data are accessible through the PRIDE repository under PXD002065.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Significance B test was used to characterize the most significantly regulated proteins after silencing of TKs (p<0.05) [8]."}, "evidence": [{"asset": "source:pmid:27054188", "locator": "sections[11] \"Bioinformatics analysis\" paragraph 2", "quote": "Significance B test was used to characterize the most significantly regulated proteins after silencing of TKs (p<0.05) [8]."}, {"asset": "source:pmid:27054188", "locator": "sections[10] \"Proteome quantification\" paragraph 2", "quote": "The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium [2] via the PRIDE partner repository with the dataset identifier PXD002065."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The paper used the Significance B test (p<0.05) to identify significantly regulated proteins, and the raw mass-spectrometry data are accessible through the PRIDE repository under PXD002065.", "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:27054188"], "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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Subsequently, bioinformatics analyses were", "ion of the 90 TKs was profiled by RT-qPCR in MCF7 cells. Next, the knock-down efficiency of a", "y RT-PCR and western blotting. Subsequently, MCF7 cells grown in either R0K0 ‘light’, or R6K4"], "order_basis": "paper_text_order:1246", "id": "assay:1"}, {"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ene expression of the 90 TKs was profiled by RT-qPCR in MCF7 cells. Next, the knock-down efficien", "expression of the 90 TKs was profiled by RT-qPCR in MCF7 cells. 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