Identification of mitochondrial disease genes through integrative analysis of multiple datasets

Methods

Volumn 46, Issue 4, 2008, Pages 248-255

  Aiyar, Raeka S ^a   Gagneur, Julien ^a   Steinmetz, Lars M ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Bayesian data integration; Discrimination analysis; Functional gene network; Functional genomics; Genetic disorder; Genome wide dataset; Machine learning; Mitochondria; Positional cloning; Support vector machine

Indexed keywords

ARTICLE; CELL FUNCTION; DATA BASE; DISORDERS OF MITOCHONDRIAL FUNCTIONS; FUNCTIONAL GENOMICS; GENE; GENE IDENTIFICATION; INTEGRATION; MITOCHONDRION; PRIORITY JOURNAL;

ALPHAPROTEOBACTERIA; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; GENES, MITOCHONDRIAL; HUMANS; MITOCHONDRIA; MITOCHONDRIAL DISEASES; PROTEIN INTERACTION MAPPING; PROTEOMICS;

EID: 56249148878     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2008.10.002     Document Type: Article

References (90)

1. Online Mendelian Inheritance in Man, OMIM (TM). McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University (Baltimore, MD) and National Center for Biotechnology Information, National Library of Medicine (Bethesda, MD), October 2, 2008. World Wide Web URL: www.ncbi.nlm.nih.gov/omim.
2. Botstein D., and Risch N. Nat. Genet. 33 Suppl. (2003) 228-237
3. Lander E.S., and Botstein D. Genetics 121 (1989) 185-199
4. Hamosh A., Scott A.F., Amberger J.S., Bocchini C.A., and McKusick V.A. Nucleic Acids Res. 33 Database Issue (2005) D514-D517
5. Dudbridge F., Gusnanto A., and Koeleman B.P. Hum. Genomics 2 (2006) 310-317
6. Hoh J., and Ott J. Nat. Rev. Genet. 4 (2003) 701-709
7. Kruglyak L. Nat. Rev. Genet. 9 (2008) 314-318
8. Prokisch H., Scharfe C., Camp D.G., Xiao W., David L., Andreoli C., Monroe M.E., Moore R.J., Gritsenko M.A., Kozany C., Hixson K.K., Mottaz H.M., Zischka H., Ueffing M., Herman Z.S., Davis R.W., Meitinger T., Oefner P.J., Smith R.D., and Steinmetz L.M. PLoS Biol. 2 (2004) e160
9. Hastie T., Tibshirani R., and Friedman J.H. The Elements of Statistical Learning (2001), Springer
10. Giallourakis C., Henson C., Reich M., Xie X., and Mootha V.K. Annu. Rev. Genomics Hum. Genet. 6 (2005) 381-406
11. Perocchi F., Mancera E., and Steinmetz L.M. Mol. Biosyst. 4 (2008) 18-29
12. Wallace D.C. Annu. Rev. Genet. 39 (2005) 359-407
13. Chan D.C. Cell 125 (2006) 1241-1252
14. Wallace D.C. Science 283 (1999) 1482-1488
15. Schaefer A.M., Taylor R.W., Turnbull D.M., and Chinnery P.F. Biochim. Biophys. Acta 1659 (2004) 115-120
16. Prokisch H., Andreoli C., Ahting U., Heiss K., Ruepp A., Scharfe C., and Meitinger T. Nucleic Acids Res. 34 (2006) D705-D711
17. Haas R.H., Parikh S., Falk M.J., Saneto R.P., Wolf N.I., Darin N., and Cohen B.H. Pediatrics 120 (2007) 1326-1333
18. Westermann B., and Neupert W. Nat. Biotechnol. 21 (2003) 239-240
19. Calvo S., Jain M., Xie X., Sheth S.A., Chang B., Goldberger O.A., Spinazzola A., Zeviani M., Carr S.A., and Mootha V.K. Nat. Genet. 38 (2006) 576-582
20. Pagliarini D.J., Calvo S.E., Chang B., Sheth S.A., Vafai S.B., Ong S.-E., Walford G.A., Sugiana C., Boneh A., Chen W.K., Hill D.E., Vidal M., Evans J.G., Thorburn D.R., Carr S.A., and Mootha V.K. Cell 134 (2008) 112-123
21. Perocchi F., Jensen L.J., Gagneur J., Ahting U., von Mering C., Bork P., Prokisch H., and Steinmetz L.M. PLoS Genet. 2 (2006) e170+
22. Vo T.D., Greenberg H.J., and Palsson B.O. J. Biol. Chem. 279 (2004) 39532-39540
23. Cotter D., Guda P., Fahy E., and Subramaniam S. Nucleic Acids Res. 32 (2004) D463-D467
24. Steinmetz L.M., Scharfe C., Deutschbauer A.M., Mokranjac D., Herman Z.S., Jones T., Chu A.M., Giaever G., Prokisch H., Oefner P.J., and Davis R.W. Nat. Genet. 31 (2002) 400-404
25. D'Elia D., Catalano D., Licciulli F., Turi A., Tripoli G., Porcelli D., Saccone C., and Caggese C. Mitochondrion 6 (2006) 252-257
26. Heazlewood J.L., and Millar A.H. Nucleic Acids Res. 33 (2005) D605-D610
27. Mootha V.K., Lepage P., Miller K., Bunkenborg J., Reich M., Hjerrild M., Delmonte T., Villeneuve A., Sladek R., Xu F., Mitchell G.A., Morin C., Mann M., Hudson T.J., Robinson B., Rioux J.D., and Lander E.S. Proc. Natl. Acad. Sci. USA 100 (2003) 605-610
28. Spinazzola A., Viscomi C., Fernandez-Vizarra E., Carrara F., D'Adamo P., Calvo S., Marsano R.M., Donnini C., Weiher H., Strisciuglio P., Parini R., Sarzi E., Chan A., Dimauro S., Rötig A., Gasparini P., Ferrero I., Mootha V.K., Tiranti V., and Zeviani M. Nat. Genet. 38 (2006) 570-575
29. DeRisi J.L., Iyer V.R., and Brown P.O. Science 278 (1997) 680-686
30. Lascaris R., Bussemaker H.J., Boorsma A., Piper M., van der Spek H., Grivell L., and Blom J. Genome Biol. 4 (2003) R3
31. D'Souza A.D., Parikh N., Kaech S.M., and Shadel G.S. Mitochondrion 7 (2007) 374-385
32. Huh W.K., Falvo J.V., Gerke L.C., Carroll A.S., Howson R.W., Weissman J.S., and O'Shea E.K. Nature 425 (2003) 686-691
33. Kumar A., Agarwal S., Heyman J.A., Matson S., Heidtman M., Piccirillo S., Umansky L., Drawid A., Jansen R., Liu Y., Cheung K.-H., Miller P., Gerstein M., Roeder S.G., and Snyder M. Genes Dev. 16 (2002) 707-719
34. Ozawa T., and Umezawa Y. Methods Mol. Biol. 390 (2007) 119-130
35. Dimmer K.S., Fritz S., Fuchs F., Messerschmitt M., Weinbach N., Neupert W., and Westermann B. Mol. Biol. Cell 13 (2002) 847-853
36. Chen J., Shi X., Padmanabhan R., Wang Q., Wu Z., Stevenson S.C., Hild M., Garza D., and Li H. Genome Res. 18 (2008) 123-136
37. R. Ichishita, K. Tanaka, Y. Sugiura, T. Sayano, K. Mihara, T. Oka, J. Biochem. (2008).
38. Emanuelsson O., Brunak S., von Heijne G., and Nielsen H. Nat. Protoc. 2 (2007) 953-971
39. Nakai K., and Horton P. Methods Mol. Biol. 390 (2007) 429-466
40. Guda C., and Subramaniam S. Bioinformatics 21 (2005) 3963-3969
41. Andrade M.A., O'Donoghue S.I., and Rost B. J. Mol. Biol. 276 (1998) 517-525
42. Emanuelsson O., Nielsen H., Brunak S., and von Heijne G. J. Mol. Biol. 300 (2000) 1005-1016
43. Hua S., and Sun Z. Bioinformatics 17 (2001) 721-728
44. Nakai K., and Horton P. Trends Biochem. Sci. 24 (1999) 34-36
45. Horton P., Park K.J., Obayashi T., Fujita N., Harada H., Adams-Collier C.J., and Nakai K. Nucleic Acids Res. 35 (2007) W585-W587
46. Small I., Peeters N., Legeai F., and Lurin C. Proteomics 4 (2004) 1581-1590
47. Sylvestre J., Margeot A., Jacq C., Dujardin G., and Corral-Debrinski M. Mol. Biol. Cell 14 (2003) 3848-3856
48. Marc P., Margeot A., Devaux F., Blugeon C., Corral-Debrinski M., and Jacq C. EMBO Rep. 3 (2002) 159-164
49. Delahunty C., and Yates III J.R. Methods 35 (2005) 248-255
50. Sickmann A., Reinders J., Wagner Y., Joppich C., Zahedi R., Meyer H.E., Schönfisch B., Perschil I., Chacinska A., Guiard B., Rehling P., Pfanner N., and Meisinger C. Proc. Natl. Acad. Sci. USA 100 (2003) 13207-13212
51. Domon B., and Aebersold R. Science 312 (2006) 212-217
52. Mootha V.K., Bunkenborg J., Olsen J.V., Hjerrild M., Wisniewski J.R., Stahl E., Bolouri M.S., Ray H.N., Sihag S., Kamal M., Patterson N., Lander E.S., and Mann M. Cell 115 (2003) 629-640
53. Da Cruz S., Parone P.A., and Martinou J.C. Expert Rev. Proteomics 2 (2005) 541-551
54. von Mering C., Krause R., Snel B., Cornell M., Oliver S.G., Fields S., and Bork P. Nature 417 (2002) 399-403
55. von Mering C., Jensen L.J., Kuhn M., Chaffron S., Doerks T., Krüger B., Snel B., and Bork P. Nucleic Acids Res. 35 (2007) D358-D362
56. Ramani A.K., Bunescu R.C., Mooney R.J., and Marcotte E.M. Genome Biol. 6 (2005)
57. Bader J.S., Chaudhuri A., Rothberg J.M., and Chant J. Nat. Biotechnol. 22 (2004) 78-85
58. Rebholz-Schuhmann D., Kirsch H., and Couto F. PLoS Biol. 3 (2005) e65
59. Jaeger S., Gaudan S., Leser U., and Schuhmann D.R. BMC Bioinformatics 9 (2008) S2
60. Shatkay H., Höglund A., Brady S., Blum T., Dönnes P., and Kohlbacher O. Bioinformatics 23 (2007) 1410-1417
61. Schölkopf B., and Smola A.J. Learning with Kernels: Support Vector Machines, Regularization, Optimization, and Beyond (Adaptive Computation and Machine Learning) (2001), The MIT Press
62. Aravind L. Genome Res. 10 (2000) 1074-1077
63. Goh K.-I., Cusick M.E., Valle D., Childs B., Vidal M., and Barabasi A.-L. Proc. Natl. Acad. Sci. USA 104 (2007) 8685-8690
64. Mcgary K., Lee I., and Marcotte E. Genome Biol. 8 (2007) R258
65. Tian W., Zhang L.V., Taşan M., Gibbons F.D., King O.D., Park J., Wunderlich Z., Cherry J.M., and Roth F.P. Genome Biol. 9 Suppl. 1 (2008) S7
66. Krogan N.J., Cagney G., Yu H., Zhong G., Guo X., Ignatchenko A., Li J., Pu S., Datta N., Tikuisis A.P., Punna T., Peregrín-Alvarez J.M., Shales M., Zhang X., Davey M., Robinson M.D., Paccanaro A., Bray J.E., Sheung A., Beattie B., Richards D.P., Canadien V., Lalev A., Mena F., Wong P., Starostine A., Canete M.M., Vlasblom J., Wu S., Orsi C., Collins S.R., Chandran S., Haw R., Rilstone J.J., Gandi K., Thompson N.J., Musso G., Onge R.P.St., Ghanny S., Lam M.H.Y., Butland G., Altaf-Ul A.M., Kanaya S., Shilatifard A., O'Shea E., Weissman J.S., Ingles J.C., Hughes T.R., Parkinson J., Gerstein M., Wodak S.J., Emili A., and Greenblatt J.F. Nature 440 (2006) 637-643
67. Tong A.H.Y., Lesage G., Bader G.D., Ding H., Xu H., Xin X., Young J., Berriz G.F., Brost R.L., Chang M., Chen Y., Cheng X., Chua G., Friesen H., Goldberg D.S., Haynes J., Humphries C., He G., Hussein S., Ke L., Krogan N., Li Z., Levinson J.N., Lu H., Menard P., Munyana C., Parsons A.B., Ryan O., Tonikian R., Roberts T., Sdicu A.-M., Shapiro J., Sheikh B., Suter B., Wong S.L., Zhang L.V., Zhu H., Burd C.G., Munro S., Sander C., Rine J., Greenblatt J., Peter M., Bretscher A., Bell G., Roth F.P., Brown G.W., Andrews B., Bussey H., and Boone C. Science 303 (2004) 808-813
68. Franke L., Bakel H., Fokkens L., de Jong E.D., Egmont-Petersen M., and Wijmenga C. Am. J. Hum. Genet. 78 (2006) 1011-1025
69. Breitkreutz B.J., Stark C., Reguly T., Boucher L., Breitkreutz A., Livstone M., Oughtred R., Lackner D.H., Bähler J., Wood V., Dolinski K., and Tyers M. Nucleic Acids Res. 36 (2008) D637-D640
70. Güldener U., Münsterkötter M., Oesterheld M., Pagel P., Ruepp A., Mewes H.W., and Stümpflen V. Nucleic Acids Res. 34 (2006) D436-D441
71. Vastrik I., D'Eustachio P., Schmidt E., Joshi-Tope G., Gopinath G., Croft D., de Bono B., Gillespie M., Jassal B., Lewis S., Matthews L., Wu G., Birney E., and Stein L. Genome Biol. 8 (2007) R39+
72. Kanehisa M., Araki M., Goto S., Hattori M., Hirakawa M., Itoh M., Katayama T., Kawashima S., Okuda S., Tokimatsu T., and Yamanishi Y. Nucleic Acids Res. 36 (2008) D480-D484
73. Jamshidi N., and Palsson B.O. Mol. Syst. Biol. 2 (2006) E1-E4
74. Mueller L.N., Brusniak M.Y., Mani D.R., and Aebersold R. J. Proteome Res. 7 (2008) 51-61
75. Marcinek D.M., Amara C., Shankland E., Schenkman K., Arakaki L., and Conley K. Methods 46 (2008) 312-318
76. Kell D.B. Drug Discov. Today 11 (2006) 1085-1092
77. Duarte N.C.C., Becker S.A.A., Jamshidi N., Thiele I., Mo M.L.L., Vo T.D.D., Srivas R., and Palsson B.O.O. Proc. Natl. Acad. Sci. USA 104 (2007) 1777-1782
78. Bundy J.G., Papp B., Harmston R., Browne R.A., Clayson E.M., Burton N., Reece R.J., Oliver S.G., and Brindle K.M. Genome Res. 17 (2007) 510-519
79. W. Song, B. Bossy, O.J. Martin, A. Hicks, S. Lubitz, A.B. Knott, E. Bossy-Wetzel, Methods, this issue, doi:10.1016/j.ymeth.2008.10.003.
80. Koopman W., Distelmaier F., Esseling J., Smeitink J., and Willems P. Methods 46 (2008) 304-311
81. Teh S.Y., Lin R., Hung L.H., and Lee A.P. Lab on a chip 8 (2008) 198-220
82. Vo T.D., Paul Lee W.N., and Palsson B.O. Mol. Genet. Metabol. 91 (2007) 15-22
83. Chen Y., Zhu J., Lum P.Y., Yang X., Pinto S., Macneil D.J., Zhang C., Lamb J., Edwards S., Sieberts S.K., Leonardson A., Castellini L.W., Wang S., Champy M.-F., Zhang B., Emilsson V., Doss S., Ghazalpour A., Horvath S., Drake T.A., Lusis A.J., and Schadt E.E. Nature 452 (2008) 429-435
84. Hood L., Heath J.R., Phelps M.E., and Lin B. Science 306 (2004) 640-643
85. The Wellcome Trust Case Control Consortium, Nature 447 (2007) 661-678.
86. Nicholson J.K. Mol. Syst. Biol. 2 (2006) 52
87. Ohlmeier S., Kastaniotis A.J., Hiltunen J.K., and Bergmann U. J. Biol. Chem. 279 (2004) 3956-3979
88. Drawid A., and Gerstein M. J. Mol. Biol. 301 (2000) 1059-1075
89. Pflieger D., Le Caer J.P., Lemaire C., Bernard B.A., Dujardin G., and Rossier J. Anal. Chem. 74 (2002) 2400-2406
90. Claros M.G. Comput. Appl. Biosci. 11 (1995) 441-447