We have developed software for phosphoproteomic site-assignment and for clustering of dynamic data. We have also developed and published software to aid in the design of peptide-directed and fusion protein-directed antibodies called NHLBI-AbDesigner (http://helixweb.nih.gov/AbDesigner/). A paper describing this tool and illustrating its use has been published (Pisitkun et al. PMID: 21956165). A second paper describing its application to development of antibodies for several glomerular marker proteins has also been published (Pisitkun et al. PMID: 25328345). NHLBI-AbDesigner is currently utilized by many commercial antibody production companies. An expansion of AbDesigner is under development. We have also developed software called PhosphoLogo to produce sequence logos from phosphoproteomic data. Current efforts are aimed at the development of practical tools for application of Bayesian statistical approaches, data-mining approaches, and structural equation modeling to large-scale physiological data. A list of available software programs can be found at http://helixweb.nih.gov/ESBL/. We have also developed several databases of proteomic and transcriptomic data to be used in kidney research (http://helixweb.nih.gov/ESBL/Database/index.html). Tools are under development for cross-referencing these databases for studies in integrative biology that are based on the Big Data concept.

Project Start
Project End
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Budget End
Support Year
5
Fiscal Year
2015
Total Cost
Indirect Cost
Name
U.S. National Heart Lung and Blood Inst
Department
Type
DUNS #
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LeMaire, Sophia M; Raghuram, Viswanathan; Grady, Cameron R et al. (2017) Serine/threonine phosphatases and aquaporin-2 regulation in renal collecting duct. Am J Physiol Renal Physiol 312:F84-F95
Corcoran, Callan C; Grady, Cameron R; Pisitkun, Trairak et al. (2017) From 20th century metabolic wall charts to 21st century systems biology: database of mammalian metabolic enzymes. Am J Physiol Renal Physiol 312:F533-F542
Hyndman, Kelly A; Knepper, Mark A (2017) Dynamic regulation of lysine acetylation: the balance between acetyltransferase and deacetylase activities. Am J Physiol Renal Physiol 313:F842-F846
Xue, Zhe; Chen, Jia-Xu; Zhao, Yue et al. (2017) Data integration in physiology using Bayes' rule and minimum Bayes' factors: deubiquitylating enzymes in the renal collecting duct. Physiol Genomics 49:151-159
Wang, Po-Jen; Lin, Shu-Ting; Liu, Shao-Hsuan et al. (2017) Vasopressin-induced serine 269 phosphorylation reduces Sipa1l1 (signal-induced proliferation-associated 1 like 1)-mediated aquaporin-2 endocytosis. J Biol Chem 292:7984-7993
Hwang, Jacqueline R; Chou, Chung-Lin; Medvar, Barbara et al. (2017) Identification of ?-catenin-interacting proteins in nuclear fractions of native rat collecting duct cells. Am J Physiol Renal Physiol 313:F30-F46
Chen, Lihe; Lee, Jae Wook; Chou, Chung-Lin et al. (2017) Transcriptomes of major renal collecting duct cell types in mouse identified by single-cell RNA-seq. Proc Natl Acad Sci U S A 114:E9989-E9998
Zhao, Yue; Yang, Chin-Rang; Raghuram, Viswanathan et al. (2016) BIG: A large-scale data integration tool for renal physiology. Am J Physiol Renal Physiol :ajprenal.00249.2016
Cheng, Lei; Pisitkun, Trairak; Knepper, Mark A et al. (2016) Peptide Labeling Using Isobaric Tagging Reagents for Quantitative Phosphoproteomics. Methods Mol Biol 1355:53-70
Pickering, Christina M; Grady, Cameron; Medvar, Barbara et al. (2016) Proteomic profiling of nuclear fractions from native renal inner medullary collecting duct cells. Physiol Genomics 48:154-66

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