In the past year, we have developed software for phosphoproteomic site-assignment and for clustering of dynamic data (in preparation for publication). 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. NHLBI-AbDesigner: An online tool for design of peptide-directed antibodies. American Journal of Physiology: Cell Physiology. Epub in advance of printing, 2011). We have also developed software to produce sequence logos from phosphoproteomic data called Phosphologo (in review). A list of available software programs can be found at http://helixweb.nih.gov/ESBL/. Finally, we have maintained an improved our proteomics and transcriptomic databases. A list of these databases can be found online at http://helixweb.nih.gov/ESBL/Database/index.html.

Project Start
Project End
Budget Start
Budget End
Support Year
2
Fiscal Year
2012
Total Cost
$174,683
Indirect Cost
Name
National Heart, Lung, and Blood Institute
Department
Type
DUNS #
City
State
Country
Zip Code
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
Huebner, Alyssa R; Cheng, Lei; Somparn, Poorichaya et al. (2016) Deubiquitylation of Protein Cargo Is Not an Essential Step in Exosome Formation. Mol Cell Proteomics 15:1556-71
Medvar, Barbara; Raghuram, Viswanathan; Pisitkun, Trairak et al. (2016) Comprehensive database of human E3 ubiquitin ligases: application to aquaporin-2 regulation. Physiol Genomics 48:502-12
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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
Yang, Chin-Rang; Tongyoo, Pumipat; Emamian, Milad et al. (2015) Deep proteomic profiling of vasopressin-sensitive collecting duct cells. I. Virtual Western blots and molecular weight distributions. Am J Physiol Cell Physiol 309:C785-98
Knepper, Mark A (2015) Systems biology of diuretic resistance. J Clin Invest 125:1793-5
Yang, Chin-Rang; Raghuram, Viswanathan; Emamian, Milad et al. (2015) Deep proteomic profiling of vasopressin-sensitive collecting duct cells. II. Bioinformatic analysis of vasopressin signaling. Am J Physiol Cell Physiol 309:C799-812
Lee, Jae Wook; Chou, Chung-Lin; Knepper, Mark A (2015) Deep Sequencing in Microdissected Renal Tubules Identifies Nephron Segment-Specific Transcriptomes. J Am Soc Nephrol 26:2669-77
Lee, Jae Wook (2015) RNA sequencing of the nephron transcriptome: a technical note. Kidney Res Clin Pract 34:219-27

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