Understanding kidney disease: Toward the integration of regulatory networks across species

Seminars in Nephrology

Volumn 30, Issue 5, 2010, Pages 512-519

  Ju, Wenjun ^a   Brosius, Frank C ^a  

^a UNIVERSITY OF MICHIGAN MEDICAL SCHOOL   (United States)

Author keywords

Chronic kidney disease; Metabolomics; Molecular marker; Network integration; Systems biology; Transcriptomics

Indexed keywords

IMIDAZOLEACETIC ACID; INDICAN; JANUS KINASE; JANUS KINASE 1; JANUS KINASE 2; JANUS KINASE 3; N METHYLFORMAMIDE; ROSIGLITAZONE; STAT PROTEIN; STAT1 PROTEIN; THIAMINE PHOSPHATE; UBIQUINONE;

ARTICLE; CHRONIC KIDNEY DISEASE; COMPARATIVE GENOMIC HYBRIDIZATION; COMPUTER INTERFACE; COMPUTER PROGRAM; DIABETIC NEPHROPATHY; DISEASE COURSE; DNA MICROARRAY; EXPRESSED SEQUENCE TAG; GENETIC ASSOCIATION; GLOMERULUS FILTRATION RATE; HUMAN; HUMAN VERSUS ANIMAL COMPARISON; KIDNEY DISEASE; KIDNEY FAILURE; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; ORTHOLOGY; PATHOPHYSIOLOGY; PRIORITY JOURNAL; PROTEIN EXPRESSION; SERIAL ANALYSIS OF GENE EXPRESSION; SIGNAL TRANSDUCTION; SYSTEM ANALYSIS; SYSTEMS BIOLOGY; TRANSCRIPTOMICS; UPREGULATION; URINALYSIS; WEB BROWSER;

ANIMALS; DISEASE MODELS, ANIMAL; DISEASE PROGRESSION; GENE REGULATORY NETWORKS; HUMANS; KIDNEY DISEASES; METABOLOMICS; MICE; SYSTEMS BIOLOGY;

EID: 78049435709     PISSN: 02709295     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.semnephrol.2010.07.008     Document Type: Article

References (50)

1. Frese K.K., Tuveson D.A. Maximizing mouse cancer models. Nat Rev Cancer 2007, 7:645-658.
2. Mattison J., van der Weyden L., Hubbard T., Adams D.J. Cancer gene discovery in mouse and man. Biochim Biophys Acta 2009, 1796:140-161.
3. He L., Sun Y., Takemoto M., et al. The glomerular transcriptome and a predicted protein-protein interaction network. J Am Soc Nephrol 2008, 19:260-268.
4. He L., Sun Y., Patrakka J., et al. Glomerulus-specific mRNA transcripts and proteins identified through kidney expressed sequence tag database analysis. Kidney Int 2007, 71:889-900.
5. Takemoto M., He L., Norlin J., et al. Large-scale identification of genes implicated in kidney glomerulus development and function. EMBO J 2006, 25:1160-1174.
6. Chabardes-Garonne D., Mejean A., Aude J.C., et al. A panoramic view of gene expression in the human kidney. Proc Natl Acad Sci U S A 2003, 100:13710-13715.
7. Higgins J.P., Wang L., Kambham N., et al. Gene expression in the normal adult human kidney assessed by complementary DNA microarray. Mol Biol Cell 2004, 15:649-656.
8. Yasuda Y., Cohen C.D., Henger A., Kretzler M. Gene expression profiling analysis in nephrology: towards molecular definition of renal disease. Clin Exp Nephrol 2006, 10:91-98.
9. Schmid H., Cohen C.D., Henger A., Schlondorff D., Kretzler M. Gene expression analysis in renal biopsies. Nephrol Dial Transplant 2004, 19:1347-1351.
10. Henger A., Schmid H., Kretzler M. Gene expression analysis of human renal biopsies: recent developments towards molecular diagnosis of kidney disease. Curr Opin Nephrol Hypertens 2004, 13:313-318.
11. Kim J.H., Ha I.S., Hwang C.I., et al. Gene expression profiling of anti-GBM glomerulonephritis model: the role of NF-kappaB in immune complex kidney disease. Kidney Int 2004, 66:1826-1837.
12. Susztak K., Bottinger E., Novetsky A., et al. Molecular profiling of diabetic mouse kidney reveals novel genes linked to glomerular disease. Diabetes 2004, 53:784-794.
13. Schanstra J.P., Bachvarova M., Neau E., Bascands J.L., Bachvarov D. Gene expression profiling in the remnant kidney model of wild type and kinin B1 and B2 receptor knockout mice. Kidney Int 2007, 72:442-454.
14. Monrad S.U., Killen P.D., Anderson M.R., Bradke A., Kaplan M.J. The role of aldosterone blockade in murine lupus nephritis. Arthritis Res Ther 2008, 10:R5.
15. Moreno S., Ibraghimov-Beskrovnaya O., Bukanov N.O. Serum and urinary biomarker signatures for rapid preclinical in vivo assessment of CDK inhibition as a therapeutic approach for PKD. Cell Cycle 2008, 7:1856-1864.
16. Liu K., Li Q.Z., Delgado-Vega A.M., et al. Kallikrein genes are associated with lupus and glomerular basement membrane-specific antibody-induced nephritis in mice and humans. J Clin Invest 2009, 119:911-923.
17. Ju W., Eichinger F., Bitzer M., et al. Renal gene and protein expression signatures for prediction of kidney disease progression. Am J Pathol 2009, 174:2073-2085.
18. Brosius F.C., Alpers C.E., Bottinger E.P., et al. Mouse models of diabetic nephropathy. J Am Soc Nephrol 2009, 20:2503-2512.
19. Berthier C.C., Zhang H., Schin M., et al. Enhanced expression of Janus kinase-signal transducer and activator of transcription pathway members in human diabetic nephropathy. Diabetes 2009, 58:469-477.
20. Qi Z., Fujita H., Jin J., et al. Characterization of susceptibility of inbred mouse strains to diabetic nephropathy. Diabetes 2005, 54:2628-2637.
21. Gurley S.B., Clare S.E., Snow K.P., et al. Impact of genetic background on nephropathy in diabetic mice. Am J Physiol 2006, 290:F214-F222.
22. Zhang H., Saha J., Byun J., et al. Rosiglitazone reduces renal and plasma markers of oxidative injury and reverses urinary metabolite abnormalities in the amelioration of diabetic nephropathy. Am J Physiol 2008, 295:F1071-F1081.
23. Tian T, Patel JM. TALE: a tool for approximate large graph matching. Paper presented at: ICDE, International Conference on Data Engineering; April 7-12, 2008, Cancún, México.
24. Sprague J., Bayraktaroglu L., Bradford Y., et al. The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. Nucleic Acids Res 2008, 36(database issue):D768-D772.
25. Sprague J., Bayraktaroglu L., Clements D., et al. The Zebrafish Information Network: the zebrafish model organism database. Nucleic Acids Res 2006, 34(database issue):D581-D585.
26. Tomancak P., Berman B.P., Beaton A., et al. Global analysis of patterns of gene expression during Drosophila embryogenesis. Genome Biol 2007, 8:R145.
27. Drysdale R. FlyBase: a database for the Drosophila research community. Methods Mol Biol 2008, 420:45-59.
28. Wilson R.J., Goodman J.L., Strelets V.B. FlyBase: integration and improvements to query tools. Nucleic Acids Res 2008, 36(database issue):D588-D593.
29. Crosby M.A., Goodman J.L., Strelets V.B., Zhang P., Gelbart W.M. FlyBase: genomes by the dozen. Nucleic Acids Res 2007, 35(database issue):D486-D491.
30. Grumbling G., Strelets V. FlyBase: anatomical data, images and queries. Nucleic Acids Res 2006, 34(database issue):D484-D488.
31. Smith C.M., Finger J.H., Hayamizu T.F., et al. The mouse Gene Expression Database (GXD): 2007 update. Nucleic Acids Res 2007, 35(database issue):D618-D623.
32. Hill D.P., Begley D.A., Finger J.H., et al. The mouse Gene Expression Database (GXD): updates and enhancements. Nucleic Acids Res 2004, 32(database issue):D568-D571.
33. Ringwald M., Mangan M.E., Eppig J.T., Kadin J.A., Richardson J.E. GXD: a gene expression database for the laboratory mouse. The Gene Expression Database Group. Nucleic Acids Res 1999, 27:106-112.
34. Richardson L., Venkataraman S., Stevenson P., et al. EMAGE mouse embryo spatial gene expression database: 2010 update. Nucleic Acids Res 2010, 38(database issue):D703-D709.
35. Venkataraman S., Stevenson P., Yang Y., et al. EMAGE-Edinburgh Mouse Atlas of Gene Expression: 2008 update. Nucleic Acids Res 2008, 36(database issue):D860-D865.
36. Christiansen J.H., Yang Y., Venkataraman S., et al. EMAGE: a spatial database of gene expression patterns during mouse embryo development. Nucleic Acids Res 2006, 34(database issue):D637-D641.
37. McMahon A.P., Aronow B.J., Davidson D.R., et al. GUDMAP: the genitourinary developmental molecular anatomy project. J Am Soc Nephrol 2008, 19:667-671.
38. Martini S., Eichinger F., Nair V., Kretzler M. Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge. Rev Endocr Metab Disord 2008, 9:267-274.
39. Kuhn A., Luthi-Carter R., Delorenzi M. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. BMC Bioinformatics 2008, 9:26.
40. Haudry Y., Berube H., Letunic I., et al. 4DXpress: a database for cross-species expression pattern comparisons. Nucleic Acids Res 2008, 36(database issue):D847-D853.
41. Salgado D., Gimenez G., Coulier F., Marcelle C. COMPARE, a multi-organism system for cross-species data comparison and transfer of information. Bioinformatics 2008, 24:447-449.
42. Chen F., Mackey A.J., Stoeckert C.J., Roos D.S. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res 2006, 34(database issue):D363-D368.
43. O'Brien K.P., Remm M., Sonnhammer E.L. Inparanoid: a comprehensive database of eukaryotic orthologs. Nucleic Acids Res 2005, 33(database issue):D476-D480.
44. Kuzniar A., van Ham R.C., Pongor S., Leunissen J.A. The quest for orthologs: finding the corresponding gene across genomes. Trends Genet 2008, 24:539-551.
45. Liu J., Ghanim M., Xue L., et al. Analysis of Drosophila segmentation network identifies a JNK pathway factor overexpressed in kidney cancer. Science 2009, 323:1218-1222.
46. Langenau D.M., Keefe M.D., Storer N.Y., et al. Effects of RAS on the genesis of embryonal rhabdomyosarcoma. Genes Dev 2007, 21:1382-1395.
47. Sreenivasan R., Cai M., Bartfai R., et al. Transcriptomic analyses reveal novel genes with sexually dimorphic expression in the zebrafish gonad and brain. PLoS One 2008, 3:e1791.
48. Kobayashi I., Ono H., Moritomo T., et al. Comparative gene expression analysis of zebrafish and mammals identifies common regulators in hematopoietic stem cells. Blood 2010, 115:e1-e9.
49. Christensen E.I., Raciti D., Reggiani L., Verroust P.J., Brandli A.W. Gene expression analysis defines the proximal tubule as the compartment for endocytic receptor-mediated uptake in the Xenopus pronephric kidney. Pflugers Arch 2008, 456:1163-1176.
50. Raciti D., Reggiani L., Geffers L., et al. Organization of the pronephric kidney revealed by large-scale gene expression mapping. Genome Biol 2008, 9:R84.