Network theory to understand microarray studies of complex diseases

Current Molecular Medicine

Volumn 6, Issue 6, 2006, Pages 695-701

  Benson, Mikael ^a   Breitling, Rainer ^b  

^a QUEEN SILVIA CHILDREN'S HOSPITAL   (Sweden)

^b UNIVERSITY OF GRONINGEN   (Netherlands)

Author keywords

Co expression; DNA microarray; Gene A; Hub proteins; Repressor Molecule Z

Indexed keywords

BIOLOGICAL MARKER; DNA; GENE PRODUCT; MESSENGER RNA; MYC PROTEIN; PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

ALLERGY; CELL FUNCTION; CONCEPTUAL FRAMEWORK; CORRELATION ANALYSIS; DIABETES MELLITUS; DISEASE ACTIVITY; DNA MICROARRAY; DRUG TARGETING; FEEDBACK SYSTEM; GENE CONTROL; GENE DELETION; GENE EXPRESSION PROFILING; GENE INTERACTION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; HUMAN; HYPOTHESIS; INDIVIDUALIZATION; LETHALITY; MUTATIONAL ANALYSIS; NETWORK MODEL; NONHUMAN; OBESITY; PATHOGENESIS; PROTEIN MODIFICATION; QUANTITATIVE TRAIT LOCUS; REVIEW; SIGNAL TRANSDUCTION; THEORETICAL MODEL; TRANSCRIPTION REGULATION; TRANSCRIPTOMICS; TRANSLATION REGULATION; TREATMENT PLANNING; YEAST CELL;

HUMANS; MODELS, BIOLOGICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RESEARCH DESIGN; SYSTEMS BIOLOGY;

EID: 33748597382     PISSN: 15665240     EISSN: None     Source Type: Journal    
DOI: 10.2174/156652406778195044     Document Type: Review

References (29)

1. Benson, M., Olsson, M., Rudemo, M., Wennergren, G. and Cardell, L. O. (2004) Clin. Exp. Allergy, 34, 1001-1006.
2. Davidson, E. H., Rast, J. P., Oliveri, P., Ransick, A., Calestani, C., Yuh, C. H., Minokawa, T., Amore, G., Hinman, V., Arenas-Mena, C., Otim, O., Brown, C. T., Livi, C. B., Lee, P. Y., Revilla, R., Rust, A. G., Pan, Z., Schilstra, M. J., Clarke, P. J., Amone, M. I., Rowen, L., Cameron, R. A., McClay, D. R., Hood, L. and Bolouri, H. (2002) Science, 295, 1669-1678.
3. Watts, D. J. and Strogatz, S. H. (1998) Nature, 393, 440-442.
4. Bar-Joseph, Z., Gerber, G. K., Lee, T. I., Rinaldi, N. J., Yoo, J. Y., Robert, F., Gordon, D. B., Fraenkel, E., Jaakkola, T. S., Young, R. A and Gifford, D. K. (2003) Nat. Biotechnol., 21, 1337-1342.
5. Qian, J., Lin, J., Luscombe, N. M., Yu, H. and Gerstein, M. (2003) Bioinformatics, 19, 1917-1926.
6. Wagner, A. (2004) J. Comput. Biol., 11, 53-60.
7. Schadt, E. E., Monks, S. A., Drake, T. A., Lusis, A. J., Che, N., Colinayo, V., Ruff, T. G., Milligan, S. B., Lamb, J. R., Cavet, G., Linsley, P. S., Mao, M., Stoughton, R. B. and Friend, S. H. (2003) Nature, 422, 297-302.
8. Chesler, E. J., Lu, L., Shou, S., Qu, Y., Gu, J., Wang, J., Hsu, H. C., Mountz, J. D., Baldwin, N. E., Langston, M. A., Threadgill, D. W., Manly, K. F. and Williams, R. W. (2005) Nat. Genet, 37, 233-242.
9. Morley, M., Molony, C. M., Weber, T. M., Devlin, J. L., Ewens, K. G., Spielman, R. S. and Cheung, V. G. (2004) Nature, 430, 743-747.
10. Wagner, A. (2001) Bioinformatics, 17, 1183-1197.
11. Barabasi, A. L. and Oltvai, Z. N. (2004) Nat. Rev. Genet., 5, 101-113.
12. Jeong, H., Mason, S. P., Barabasi, A. L. and Oltvai, Z. N. (2001) Nature, 411, 41-42.
13. Wit, E. and Khanin, R. (2006) J. Comput. Biol., 13(3), 810-818.
14. Mangan, S. and Alon, U. (2003) Proc. Natl. Acad. Sci. USA, 100, 11980-11985.
15. Carter, S. L., Brechbuhler, C. M., Griffin, M. and Bond, A. T. (2004) Bioinformatics, 20, 2242-2250.
16. Stuart, J. M., Segal, E., Koller, D. and Kim, S. K. (2003) Science, 302, 249-255.
17. Bergmann, S., Ihmels, J. and Barkai, N. (2004) PLoS Biol., 2, E9.
18. Lee, H. K., Hsu, A. K., Sajdak, J., Qin, J. and Pavlidis, P. (2004) Genome Res., 14, 1085-1094.
19. Sweet-Cordero, A., Mukherjee, S., Subramanian, A., You, H., Roix, J. J., Ladd-Acosta, C., Mesirov, J., Golub, T. R. and Jacks, T. (2005) Nat. Genet., 37, 48-55.
20. Segal, E., Friedman, N., Kaminski, N., Regev, A. and Koller, D. (2005) Nat. Genet., 37 Suppl, S38-45.
21. Basso, K., Margolin, A. A., Stolovitzky, G., Klein, U., Dalla-Favera, R. and Califano, A. (2005) Nat. Genet., 37, 382-390.
22. Levens, D. (2002) Proc. Natl. Acad. Sci. USA, 99, 5757-5759.
23. van Steensel, B. (2005) Nat. Genet., 37 Suppl, S18-24.
24. Mootha, V. K., Lindgren, C. M., Eriksson, K. F., Subramanian, A., Sihag, S., Lehar, J., Puigserver, P., Carlsson, E., Ridderstrale, M., Laurila, E., Houstis, N., Daly, M. J., Patterson, N., Mesirov, J. P., Golub, T. R., Tamayo, P., Spiegelman, B., Lander, E. S., Hirschhorn, J. N., Altshuler, D. and Groop, L. C. (2003) Nat. Genet., 34, 267-273.
25. Tong, A. H., Lesage, G., Bader, G. D., Ding, H., Xu, H., Xin, X., Young, J., Berriz, G. F., Brost, R. L., Chang, M., Chen, Y., Chang, 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. (2004) Science, 303, 808-813.
26. Kajiwara, K., Berson, E. L. and Dryja, T. P. (1994) Science, 264, 1604-1608.
27. Wagner, A. (2005) Mol. Biol. Evol., 22, 1365-1374.
28. Stuart, R. O., Wachsman, W., Berry, C. C., Wang-Rodriguez, J., Wasserman, L., Klacansky, I., Masys, D., Arden, K., Goodison, S., McClelland, M., Wang, Y., Sawyers, A., Kalcheva, I., Tarin, D. and Mercola, D. (2004) Proc. Natl. Acad. Sci. USA, 101, 615-620.
29. Garber, K. (2004) Science, 303, 1754-1755.