Literature DB >> 22114206

Gene expression databases for kidney epithelial cells.

Jennifer C Huling1, Trairak Pisitkun, Jae H Song, Ming-Jiun Yu, Jason D Hoffert, Mark A Knepper.   

Abstract

The 21st century has seen an explosion of new high-throughput data from transcriptomic and proteomic studies. These data are highly relevant to the design and interpretation of modern physiological studies but are not always readily accessible to potential users in user-friendly, searchable formats. Data from our own studies involving transcriptomic and proteomic profiling of renal tubule epithelia have been made available on a variety of online databases. Here, we provide a roadmap to these databases and illustrate how they may be useful in the design and interpretation of physiological studies. The databases can be accessed through http://helixweb.nih.gov/ESBL/Database.

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Year:  2011        PMID: 22114206      PMCID: PMC3289419          DOI: 10.1152/ajprenal.00457.2011

Source DB:  PubMed          Journal:  Am J Physiol Renal Physiol        ISSN: 1522-1466


  28 in total

1.  A panoramic view of gene expression in the human kidney.

Authors:  Danielle Chabardès-Garonne; Arnaud Mejéan; Jean-Christophe Aude; Lydie Cheval; Antonio Di Stefano; Marie-Claude Gaillard; Martine Imbert-Teboul; Monika Wittner; Chanth Balian; Véronique Anthouard; Catherine Robert; Beatrice Ségurens; Patrick Wincker; Jean Weissenbach; Alain Doucet; Jean-Marc Elalouf
Journal:  Proc Natl Acad Sci U S A       Date:  2003-10-31       Impact factor: 11.205

2.  In vacuo isotope coded alkylation technique (IVICAT); an N-terminal stable isotopic label for quantitative liquid chromatography/mass spectrometry proteomics.

Authors:  Brigitte L Simons; Guanghui Wang; Rong-Fong Shen; Mark A Knepper
Journal:  Rapid Commun Mass Spectrom       Date:  2006       Impact factor: 2.419

Review 3.  Global analysis of gene expression in mammalian kidney.

Authors:  Olga Soutourina; Lydie Cheval; Alain Doucet
Journal:  Pflugers Arch       Date:  2004-12-21       Impact factor: 3.657

Review 4.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors:  S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

5.  Quantitative phosphoproteomics of vasopressin-sensitive renal cells: regulation of aquaporin-2 phosphorylation at two sites.

Authors:  Jason D Hoffert; Trairak Pisitkun; Guanghui Wang; Rong-Fong Shen; Mark A Knepper
Journal:  Proc Natl Acad Sci U S A       Date:  2006-04-25       Impact factor: 11.205

6.  Large scale protein identification in intracellular aquaporin-2 vesicles from renal inner medullary collecting duct.

Authors:  Maria Barile; Trairak Pisitkun; Ming-Jiun Yu; Chung-Lin Chou; Michael J Verbalis; Rong-Fong Shen; Mark A Knepper
Journal:  Mol Cell Proteomics       Date:  2005-05-18       Impact factor: 5.911

7.  Transcriptome of a mouse kidney cortical collecting duct cell line: effects of aldosterone and vasopressin.

Authors:  M Robert-Nicoud; M Flahaut; J M Elalouf; M Nicod; M Salinas; M Bens; A Doucet; P Wincker; F Artiguenave; J D Horisberger; A Vandewalle; B C Rossier; D Firsov
Journal:  Proc Natl Acad Sci U S A       Date:  2001-02-20       Impact factor: 11.205

8.  High-throughput identification of IMCD proteins using LC-MS/MS.

Authors:  Trairak Pisitkun; Jared Bieniek; Dmitry Tchapyjnikov; Guanghui Wang; Wells W Wu; Rong-Fong Shen; Mark A Knepper
Journal:  Physiol Genomics       Date:  2006-01-31       Impact factor: 3.107

9.  Combined proteomics and pathways analysis of collecting duct reveals a protein regulatory network activated in vasopressin escape.

Authors:  Ewout J Hoorn; Jason D Hoffert; Mark A Knepper
Journal:  J Am Soc Nephrol       Date:  2005-08-03       Impact factor: 10.121

10.  Proteomic analysis of long-term vasopressin action in the inner medullary collecting duct of the Brattleboro rat.

Authors:  Bas W M van Balkom; Jason D Hoffert; Chung-Lin Chou; Mark A Knepper
Journal:  Am J Physiol Renal Physiol       Date:  2003-10-07
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  20 in total

1.  Application of systems biology principles to protein biomarker discovery: urinary exosomal proteome in renal transplantation.

Authors:  Trairak Pisitkun; Maria T Gandolfo; Samarjit Das; Mark A Knepper; Serena M Bagnasco
Journal:  Proteomics Clin Appl       Date:  2012-06       Impact factor: 3.494

2.  Role of Nox4 and p67phox subunit of Nox2 in ROS production in response to increased tubular flow in the mTAL of Dahl salt-sensitive rats.

Authors:  Nadezhda N Zheleznova; Chun Yang; Allen W Cowley
Journal:  Am J Physiol Renal Physiol       Date:  2016-06-08

Review 3.  Systems biology in physiology: the vasopressin signaling network in kidney.

Authors:  Mark A Knepper
Journal:  Am J Physiol Cell Physiol       Date:  2012-08-29       Impact factor: 4.249

4.  Proteomic profiling and pathway analysis of the response of rat renal proximal convoluted tubules to metabolic acidosis.

Authors:  Kevin L Schauer; Dana M Freund; Jessica E Prenni; Norman P Curthoys
Journal:  Am J Physiol Renal Physiol       Date:  2013-06-26

5.  Prostaglandin E2 EP3 receptor regulates cyclooxygenase-2 expression in the kidney.

Authors:  Carlos P Vio; Mariana Quiroz-Munoz; Catherina A Cuevas; Carlos Cespedes; Nicholas R Ferreri
Journal:  Am J Physiol Renal Physiol       Date:  2012-05-23

6.  BIG: a large-scale data integration tool for renal physiology.

Authors:  Yue Zhao; Chin-Rang Yang; Viswanathan Raghuram; Jaya Parulekar; Mark A Knepper
Journal:  Am J Physiol Renal Physiol       Date:  2016-06-08

7.  MARCKS-related protein regulates cytoskeletal organization at cell-cell and cell-substrate contacts in epithelial cells.

Authors:  Christina M Van Itallie; Amber Jean Tietgens; Angel Aponte; Marjan Gucek; Alexander X Cartagena-Rivera; Richard S Chadwick; James M Anderson
Journal:  J Cell Sci       Date:  2018-02-02       Impact factor: 5.285

8.  Vasopressin-induced serine 269 phosphorylation reduces Sipa1l1 (signal-induced proliferation-associated 1 like 1)-mediated aquaporin-2 endocytosis.

Authors:  Po-Jen Wang; Shu-Ting Lin; Shao-Hsuan Liu; Kuang-Ting Kuo; Chun-Hua Hsu; Mark A Knepper; Ming-Jiun Yu
Journal:  J Biol Chem       Date:  2017-03-23       Impact factor: 5.157

9.  The N and C termini of ZO-1 are surrounded by distinct proteins and functional protein networks.

Authors:  Christina M Van Itallie; Angel Aponte; Amber Jean Tietgens; Marjan Gucek; Karin Fredriksson; James Melvin Anderson
Journal:  J Biol Chem       Date:  2013-04-03       Impact factor: 5.157

10.  Complement C1r serine protease contributes to kidney fibrosis.

Authors:  Sandhya Xavier; Ranjit K Sahu; Sai Vineela Bontha; Valeria Mass; Ronald P Taylor; Judit Megyesi; Nicole M Thielens; Didier Portilla
Journal:  Am J Physiol Renal Physiol       Date:  2019-09-11
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