The KUPKB: A novel Web application to access multiomics data on kidney disease

FASEB Journal

Volumn 26, Issue 5, 2012, Pages 2145-2153

  Klein, Julie ^a,b   Jupp, Simon ^c   Moulos, Panagiotis ^a,b   Fernandez, Myriem ^a,b   Buffin Meyer, Bénédicte ^a,b   Casemayou, Audrey ^a,b   Chaaya, Rana ^a,b   Charonis, Aristidis ^d   Bascands, Jean Loup ^a,b   Stevens, Robert ^c   Schanstra, Joost P ^a,b  

^a Université de Toulouse   (France)

^b UNIVERSITÉ PAUL SABATIER   (France)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

^d BIOMEDICAL RESEARCH FOUNDATION   (Greece)

Author keywords

Bioinformatics; Experimental data; Genomics; Proteomics; Renal pathophysiology

Indexed keywords

CALRETICULIN; MESSENGER RNA; MICRORNA; PROTEIN DERIVATIVE;

ANIMAL EXPERIMENT; ANIMAL MODEL; ANIMAL TISSUE; ARTICLE; CHRONIC GRAFT REJECTION; CONTROLLED STUDY; DATA BASE; HUMAN; HUMAN TISSUE; IMMUNOHISTOCHEMISTRY; INTERNET; KIDNEY DISEASE; KIDNEY FIBROSIS; KIDNEY GRAFT REJECTION; MALE; METABOLITE; NONHUMAN; PATHOPHYSIOLOGY; PRIORITY JOURNAL; PROTEOMICS; PUBLICATION; RAT; VALIDATION PROCESS;

ANIMALS; CALRETICULIN; DATABASES, FACTUAL; DISEASE MODELS, ANIMAL; HUMANS; IMMUNOHISTOCHEMISTRY; INTERNET; KIDNEY DISEASES; MALE; RATS; RATS, SPRAGUE-DAWLEY;

RATTUS;

EID: 84860913822     PISSN: 08926638     EISSN: 15306860     Source Type: Journal    
DOI: 10.1096/fj.11-194381     Document Type: Article

References (35)

1. Stevens, R. D., Tipney, H. J., Wroe, C. J., Oinn, T. M., Senger, M., Lord, P. W., Goble, C. A., Brass, A., and Tassabehji, M. (2004) Exploring Williams-Beuren syndrome using myGrid. Bioinformatics 20(Suppl. 1), i303-i310 (Pubitemid 41296703)
2. Miyamoto, M., Yoshida, Y., Taguchi, I., Nagasaka, Y., Tasaki, M., Zhang, Y., Xu, B., Nameta, M., Sezaki, H., Cuellar, L. M., Osawa, T., Morishita, H., Sekiyama, S., Yaoita, E., Kimura, K., and Yamamoto, T. (2007) In-depth proteomic profiling of the normal human kidney glomerulus using two-dimensional protein prefractionation in combination with liquid chromatography-tandem mass spectrometry. J. Proteome Res. 6, 3680-3690 (Pubitemid 47522757)
3. Harding, S. D., Armit, C., Armstrong, J., Brennan, J., Cheng, Y., Haggarty, B., Houghton, D., Lloyd-Macgilp, S., Pi, X., Roochun, Y., Sharghi, M., Tindal, C., McMahon, A. P., Gottesman, B., Little, M. H., Georgas, K., Aronow, B. J., Potter, S. S., Brunskill, E. W., Southard-Smith, E. M., Mendelsohn, C., Baldock, R. A., Davies, J. A., and Davidson, D. (2011) The GUDMAP database-an online resource for genitourinary research. Development 138, 2845-2853
4. Pisitkun, T., Bieniek, J., Tchapyjnikov, D., Wang, G., Wu, W. W., Shen, R. F., and Knepper, M. A. (2006) High-throughput identification of IMCD proteins using LC-MS/MS. Physiol. Genomics 25, 263-276
5. Davidson, S. B., Overton, C., and Buneman, P. (1995) Challenges in integrating biological data sources. J. Comput. Biol. 2, 557-572
6. Goble, C., and Stevens, R. (2008) State of the nation in data integration for bioinformatics. J. Biomed. Inform. 41, 687-693
7. Kypreou, K. P., Kavvadas, P., Karamessinis, P., Peroulis, M., Alberti, A., Sideras, P., Psarras, S., Capetanaki, Y., Politis, P. K., and Charonis, A. S. (2008) Altered expression of calreticulin during the development of fibrosis. Proteomics 8, 2407-2419
8. Shadbolt, N. H. W., and Berners-Lee, T. (2006) The semantic web revisited. Intelligent systems. IEEE 21, 96-101
9. Jupp, S., Klein, J., Schanstra, J., and Stevens, R. (2011) Developing a kidney and urinary pathway knowledge base. J. Biomed. Semantics 2(Suppl. 2), S7
10. Stevens, R. A. M., Wolstencroft, K., Sattler, U., Drummond, N., Horridge, M., and Rector, A. (2007) Using OWL to model biological knowledge. Int. J. Human Comput. Studies 65, 583-594 (Pubitemid 46803278)
11. Renal GO Working Group. GO Annotation for the Renal System. Available at: http://www.geneontology.org/GO.renal.shtml
12. Hayamizu, T. F., Mangan, M., Corradi, J. P., Kadin, J. A., and Ringwald, M. (2005) The Adult Mouse Anatomical Dictionary: a tool for annotating and integrating data. Genome Biol. 6, R29
13. Bard, J., Rhee, S. Y., and Ashburner, M. (2005) An ontology for cell types. Genome Biol. 6, R21
14. Harris, M. A., Clark, J., Ireland, A., Lomax, J., Ashburner, M., Foulger, R., Eilbeck, K., Lewis, S., Marshall, B., Mungall, C., Richter, J., Rubin, G. M., Blake, J. A., Bult, C., Dolan, M., Drabkin, H., Eppig, J. T., Hill, D. P., Ni, L., Ringwald, M., Balakrishnan, R., Cherry, J. M., Christie, K. R., Costanzo, M. C., Dwight, S. S., Engel, S., Fisk, D. G., Hirschman, J. E., Hong, E. L., Nash, R. S., Sethuraman, A., Theesfeld, C. L., Botstein, D., Dolinski, K., Feierbach, B., Berardini, T., Mundodi, S., Rhee, S. Y., Apweiler, R., Barrell, D., Camon, E., Dimmer, E., Lee, V., Chisholm, R., Gaudet, P., Kibbe, W., Kishore, R., Schwarz, E. M., Sternberg, P., Gwinn, M., Hannick, L., Wortman, J., Berriman, M., Wood, V., de la Cruz, N., Tonellato, P., Jaiswal, P., Seigfried, T., and White, R. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res. 32, D258-261 (Pubitemid 38081651)
15. World Wide Web Consortium. W3C Recommendation. Retrieved February 9, 2012, from http://www.w3.org/TR/rdf-primer
16. Belleau, F., Nolin, M. A., Tourigny, N., Rigault, P., and Morissette, J. (2008) Bio2RDF: towards a mashup to build bioinformatics knowledge systems. J. Biomed. Inform. 41, 706-716
17. Ruttenberg, A. R. J., Stephens, S., Samwald, M., and Cheung, K. H. A. (2008, June 4) A Prototype Knowldege Base for the Life Sciences. W3C Interest Group. Available at: http://www.w3.org/TR/hcls-kb/
18. National Center for Biotechnology Information. Entrez Gene. Retrieved February 9, 2012, from http://www.ncbi.nlm.nih.gov/gene
19. Universal Protein Resource Consortium. UniProt Knowledge Base. Retrieved February 9, 2012, from http://www.uniprot.org
20. European Molecular Biology Laboratory-European Bioinformatics Institute. MicroCosm Targets Version 5. Retrieved February 2012, from http://www.ebi.ac.uk/ enright-srv/microcosm/htdocs/targets/v5/
21. National Center for Biotechnology Information. HomoloGene. Retrieved February 9, 2012, from http://www.ncbi.nlm.nih.gov/homologene
22. Baron, D., Bihouee, A., Teusan, R., Dubois, E., Savagner, F., Steenman, M., Houlgatte, R., and Ramstein, G. (2011) MADGene: retrieval and processing of gene identifier lists for the analysis of heterogeneous microarray data sets. Bioinformatics 27, 725-726
23. Chatziioannou, A., Moulos, P., and Kolisis, F. N. (2009) Gene ARMADA: an integrated multi-analysis platform for microarray data implemented in MATLAB. BMC Bioinformatics 10, 354
24. Chaaya, R., Alfarano, C., Guilbeau-Frugier, C., Coatrieux, C., Kesteman, A. S., Parini, A., Fares, N., Gue, M., Schanstra, J. P., and Bascands, J. L. (2011) Pargyline reduces renal damage associated with ischaemia-reperfusion and cyclosporin. Nephrol. Dial. Transplant. 26, 489-498
25. Klein, J., Gonzalez, J., Decramer, S., Bandin, F., Neau, E., Salant, D. J., Heeringa, P., Pesquero, J. B., Schanstra, J. P., and Bascands, J. L. (2010) Blockade of the kinin B1 receptor ameloriates glomerulonephritis. J. Am. Soc. Nephrol. 21, 1157-1164
26. Hills, C. E., Willars, G. B., and Brunskill, N. J. (2010) Proinsulin C-peptide antagonizes the profibrotic effects of TGF-beta1 via up-regulation of retinoic acid and HGF-related signaling pathways. Mol. Endocrinol. 24, 822-831
27. Chen, Y. X., Li, Y., Wang, W. M., Zhang, W., Chen, X. N., Xie, Y. Y., Lu, J., Huang, Q. H., and Chen, N. (2010) Phosphoproteomic study of human tubular epithelial cell in response to transforming growth factor-beta-1-induced epithelial-to-mesenchymal transition. Am. J. Nephrol. 31, 24-35
28. Mueller, C. F., Wassmann, K., Berger, A., Holz, S., Wassmann, S., and Nickenig, G. (2008) Differential phosphorylation of calreticulin affects AT1 receptor mRNA stability in VSMC. Biochem. Biophys. Res. Commun. 370, 669-674
29. Barati, M. T., Merchant, M. L., Kain, A. B., Jevans, A. W., McLeish, K. R., and Klein, J. B. (2007) Proteomic analysis defines altered cellular redox pathways and advanced glycation end-product metabolism in glomeruli of db/db diabetic mice. Am. J. Physiol. Renal Physiol. 293, F1157-F1165 (Pubitemid 47583949)
30. Nakorchevsky, A., Hewel, J. A., Kurian, S. M., Mondala, T. S., Campbell, D., Head, S. R., Marsh, C. L., Yates, J. R., 3rd, and Salomon, D. R. (2010) Molecular mechanisms of chronic kidney transplant rejection via large-scale proteogenomic analysis of tissue biopsies. J. Am. Soc. Nephrol. 21, 362-373
31. Laughery, M. D., Clifford, R. J., Chi, Y., and Kaplan, J. H. (2007) Selective basolateral localization of overexpressed Na-K-ATPase beta1- and beta2- subunits is disrupted by butryate treatment of MDCK cells. Am. J. Physiol. Renal Physiol. 292, F1718-F1725 (Pubitemid 47105361)
32. Xu, Y., Wan, J., Jiang, D., and Wu, X. (2009) BMP-7 counteracts TGF-beta1-induced epithelial-to-mesenchymal transition in human renal proximal tubular epithelial cells. J. Nephrol. 22, 403-410
33. Rajasekaran, S. A., Huynh, T. P., Wolle, D. G., Espineda, C. E., Inge, L. J., Skay, A., Lassman, C., Nicholas, S. B., Harper, J. F., Reeves, A. E., Ahmed, M. M., Leatherman, J. M., Mullin, J. M., and Rajasekaran, A. K. (2010) Na,K-ATPase subunits as markers for epithelial-mesenchymal transition in cancer and fibrosis. Mol. Cancer Ther. 9, 1515-1524
34. Zeisberg, M., Bonner, G., Maeshima, Y., Colorado, P., Muller, G. A., Strutz, F., and Kalluri, R. (2001) Renal fibrosis: collagen composition and assembly regulates epithelial-mesenchymal transdifferentiation. Am. J. Pathol. 159, 1313-1321 (Pubitemid 32947961)
35. Weiss, R. H., and Kim, K. (2011) Metabolomics in the study of kidney diseases. Nat. Rev. Nephrol. 8, 22-33