Hepatic SILAC proteomic data from PANDER transgenic model.

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Burkhardt (2016)) [1], and was generated by \"spike-in\" SILAC-based proteomic analysis of livers obtained from the PANcreatic-Derived factor (PANDER) transgenic mouse (PANTG) under various metabolic conditions [1]. The mass spectrometry output of the PANTG and wild-type B6SJLF mice liver tissue and resulting proteome search from MaxQuant 1.2.2.5 employing the Andromeda search algorithm against the UniprotKB reference database for Mus musculus has been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository with dataset identifiers PRIDE: PXD004171 and doi:10.6019/PXD004171. Protein ratio values representing PANTG/wild-type obtained by MaxQuant analysis were input into the Perseus processing suite to determine statistical significance using the Significance A outlier test (p<0.05). Differentially expressed proteins using this approach were input into Ingenuity Pathway Analysis to determined altered pathways and upstream regulators that were altered in PANTG mice.", "claims": [{"id": "claim-method", "statement": "Statistical analysis was performed using the Significance A outlier test where statistical significance based on magnitude fold-change was established at p<0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27642623", "locator": "sections[10] \"LC-MS/MS, data processing and pathway analysis\" paragraph 2", "quote": "Statistical analysis was performed using the Significance A outlier test where statistical significance based on magnitude fold-change was established at p<0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data available within this article and through the ProteomeXchange Consortium via the PRIDE partner repository with dataset identifiers PRIDE:PXD004171: Proteomic Evaluation of PANDER TG Mice, Projectdoi:10.6019/PXD004171, Username: reviewer56976@ebi.ac.uk, Password: VtR5rnIR", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:27642623", "locator": "sections[2] \"table-wrap\" paragraph 1", "quote": "Data available within this article and through the ProteomeXchange Consortium via the PRIDE partner repository with dataset identifiers PRIDE:PXD004171: Proteomic Evaluation of PANDER TG Mice, Projectdoi:10.6019/PXD004171, Username: reviewer56976@ebi.ac.uk, Password: VtR5rnIR"}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified differentially expressed proteins using the Perseus Significance A outlier test at p<0.05 on MaxQuant-derived PANTG/wild-type protein ratios, and deposited the source data in PRIDE under PXD004171.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Protein ratio values representing PANTG/wild-type obtained by MaxQuant analysis were input into the Perseus processing suite to determine statistical significance using the Significance A outlier test (p<0.05)."}, "evidence": [{"asset": "source:pmid:27642623", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Protein ratio values representing PANTG/wild-type obtained by MaxQuant analysis were input into the Perseus processing suite to determine statistical significance using the Significance A outlier test (p<0.05)."}, {"asset": "source:pmid:27642623", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The mass spectrometry output of the PANTG and wild-type B6SJLF mice liver tissue and resulting proteome search from MaxQuant 1.2.2.5 employing the Andromeda search algorithm against the UniprotKB reference database for Mus musculus has been deposited to the ProteomeXchange Consortium (http://www.proteomexchange.org) via the PRIDE partner repository with dataset identifiers PRIDE: PXD004171 and doi:10.6019/PXD004171."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study identified differentially expressed proteins using the Perseus Significance A outlier test at p<0.05 on MaxQuant-derived PANTG/wild-type protein ratios, and deposited the source data in PRIDE under PXD004171.", "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:27642623"], "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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