Transitive functional annotation by shortest-path analysis of gene expression data

Proceedings of the National Academy of Sciences of the United States of America

Volumn 99, Issue 20, 2002, Pages 12783-12788

  Zhou, Xianghong ^a   Kao, Ming Chih J ^a   Wong, Wing Hung ^a,b  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ARTICLE; CONTROLLED STUDY; CORRELATION ANALYSIS; DATA BASE; DNA MICROARRAY; GENE EXPRESSION; GENE FUNCTION; GENOME; NONHUMAN; PRIORITY JOURNAL; YEAST;

CELL NUCLEUS; CYTOPLASM; DATABASES; DNA; GENE EXPRESSION; GENETIC TECHNIQUES; GENOME, FUNGAL; MITOCHONDRIA; OPEN READING FRAMES; PROTEINS; SACCHAROMYCES CEREVISIAE; STATISTICS;

SACCHAROMYCES;

EID: 0036790999     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.192159399     Document Type: Article

References (27)

1. Eisen, M. B., Spellman, P. T., Brown, P. O. & Botstein, D. (1998) Proc. Natl. Acad. Sci. USA 95, 14863-14868.
2. Tavazoie, S., Hughes, J. D., Campbell, M. J., Cho, R. J. & Church, G. M. (1999) Nat. Genet. 22, 281-285.
3. Golub, T. R., Slonim, D. K., Tamayo, P., Huard, C., Gaasenbeek, M., Mesirov, J. P., Coller, H., Loh, M. L., Downing, J. R., Caligiuri, M. A., et al. (1999) Science 286, 531-537.
4. Niehrs, C. & Poller, N. (1999) Nature (London) 402, 483-487.
5. Qian, J., Dolled-Filhart, M., Lin, J., Yu, H. & Gerstein, M. (2001) J. Mol. Biol. 314, 1053-1066.
6. Hughes, T. R., Marton, M. J., Jones, A. R., Roberts, C. J., Stoughton, R., Armour, C. D., Bennett, H. A., Coffey, E., Dai, H., He, Y. D., et al. (2000) Cell 102, 109-126.
7. Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., et al. (2000) Nat. Genet. 25, 25-29.
8. Dwight, S. S., Harris, M. A., Dolinski, K., Ball, C. A., Binkley, G., Christie, K. R., Fisk, D. G., Issel-Tarver, L., Schroeder, M., Sherlock, G., et al. (2002) Nucleic Acids Res. 30, 69-72.
9. Cormen, T. H. (2001) Introduction to Algorithms (MIT Press, Cambridge, MA).
10. Hvidsten, T. R., Komorowski, J., Sandvik, A. K. & Laegreid, A. (2001) Pac. Symp. Biocomput., 299-310.
11. Pestov, D. G., Stockelman, M. G., Strezoska, Z. & Lau, L. F. (2001) Nucleic Acids Res. 29, 3621-3630.
12. Clarke, P. R. & Zhang, C. (2001) Trends Cell Biol. 11, 366-371.
13. Milkereit, P., Gadal, O., Podtelejnikov, A., Trumtel, S., Gas, N., Petfalski, E., Tollervey, D., Mann, M., Hurt, E. & Tschochner, H. (2001) Cell 105, 499-509.
14. Osherovich, L. Z. & Weissman, J. S. (2001) Cell 106, 183-194.
15. Shumov, N. N., Volkov, K. V. & Mironova, L. N. (2000) Genetika 36, 644-650.
16. Jelinsky, S. A., Estep, P., Church, G. M. & Samson, L. D. (2000) Mol. Cell. Biol. 20, 8157-8167.
17. Kaser, A., Bogengruber, E., Hallegger, M., Doppler, E., Lepperdinger, G., Jantsch, M., Breitenbach, M. & Kreil, G. (2001) Biol. Chem. 382, 1637-1647.
18. Velculescu, V. E., Zhang, L., Zhou, W., Vogelstein, J., Basrai, M. A., Bassett, D. E., Jr., Hieter, P., Vogelstein, B. & Kinzler, K. W. (1997) Cell 88, 243-251.
19. Fujimori, F., Gunji, W., Kikuchi, J., Mogi, T., Ohashi, Y., Makino, T., Oyama, A., Okuhara, K., Uchida, T. & Murakami, Y. (2001) Biochem. Biophys. Res. Commun. 289, 181-190.
20. Bassler, J., Grandi, P., Gadal, O., Lessmann, T., Petfalski, E., Tollervey, D., Lechner, J. & Hurt, E. (2001) Mol. Cell 8, 517-529.
21. Saveanu, C., Fromont-Racine, M., Harington, A., Ricard, F., Namane, A. & Jacquier, A. (2001) J. Biol. Chem. 276, 15861-15867.
22. Mewes, H. W., Frishman, D., Guldener, U., Mannhaupt, G., Mayer, K., Mokrejs, M., Morgenstern, B., Munsterkotter, M., Rudd, S. & Weil, B. (2002) Nucleic Acids Res. 30, 31-34.
23. Causton, H. C., Ren, B., Koh, S. S., Harbison, C. T., Kanin, E., Jennings, E. G., Lee, T. I., True, H. L., Lander, E. S. & Young, R. A. (2001) Mol Biol. Cell 12, 323-337.
24. Lee, J., Godon, C., Lagniel, G., Spector, D., Garin, J., Labarre, J. & Toledano, M. B. (1999) J. Biol. Chem. 274, 16040-16046.
25. Spellman, P. T., Sherlock, G., Zhang, M. Q., Iyer, V. R., Anders, K., Eisen, M. B., Brown, P. O., Botstein, D. & Futcher, B. (1998) Mol Biol. Cell 9, 3273-3297.
26. Traven, A., Wong, J. M., Xu, D., Sopta, M. & Ingles, C. J. (2001) J. Biol. Chem. 276, 4020-4027.
27. Rep, M., Krantz, M., Thevelein, J. M. & Hohmann, S. (2000) J. Biol. Chem. 275, 8290-8300.