Whole-genome comparative annotation and regulatory motif discovery in multiple yeast species

Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB

Volumn , Issue , 2003, Pages 157-166

  Kamvysselis, Manolis ^a,b   Patterson, Nick ^a   Birren, Bruce ^a   Berger, Bonnie ^b,c   Lander, Eric ^a,c  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^c MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Comparative genomics; Computational biology; Genome annotation; Regulatory motif discovery

Indexed keywords

DNA SEQUENCES; GENETIC ENGINEERING; YEAST;

COMPUTATIONAL BIOLOGY;

GENETIC ALGORITHMS;

EID: 0037701023     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/640075.640096     Document Type: Conference Paper

References (29)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. Basic local alignment search tool. J Mol Biol, 275 (3). 403-410.
2. 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., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M. and Sherlock, G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 25 (1). 25-29.
3. Blanchette, M., Schwikowski, B. and Tompa, M. Algorithms for phylogenetic footprinting. J Comput Biol, 9 (2). 211-223.
4. Cliften, P.F., Hillier, L.W., Fulton, L., Graves, T., Miner, T., Gish, W.R., Waterston, R.H. and Johnston, M. Surveying Saccharomyces genomes to identify functional elements by comparative DNA sequence analysis. Genome Res, 11 (7). 1175-1186.
5. 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., Sethuraman, A., Weng, S., Botstein, D. and Cherry, J.M. Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO). Nucleic Acids Res, 30 (1). 69-72.
6. Fitch, W.M. Distinguishing homologous from analogous proteins. Syst Zool, 19 (2). 99-113.
7. Fitch, W.M. Uses for evolutionary trees. Philos Trans R Soc Land B Biol Sci, 349 (1327). 93-102.
8. Gasch, A.P. and Eisen, M.B. Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol, 3 (11). RESEARCH0059.
9. Gavin, A.C., Bosche, M., Krause, R., Grandi, P., Marzioch, M., Bauer, A., Schultz, J., Rick, J.M., Michon, A.M., Cruciat, C.M., Remor, M., Hofert, C., Schelder, M., Brajenovic, M., Ruffner, H., Merino, A., Klein, K., Hudak, M., Dickson, D., Rudi, T., Gnau, V., Bauch, A., Bastuck, S., Huhse, B., Leutwein, C., Heurtier, M.A., Copley, R.R., Edelmann, A., Querfurth, E., Rybin, V., Drewes, G., Raida, M., Bouwmeester, T., Bork, P., Seraphin, B., Kuster, B., Neubauer, G. and Superti-Furga, G. Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415 (6868). 141-147.
10. Grundy, W.N., Bailey, T.L., Elkan, C.P. and Baker, M.E. Meta-MEME: motif-based hidden Markov models of protein families. Comput Appl Biosci, 13 (4). 397-406.
11. Hughes, J.D., Estep, P.W., Tavazoie, S. and Church, G.M. Computational identification of cis-regulatory elements ssociated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol, 296 (5). 1205-1214.
12. Jiao, K., Nau, J.J., Cool, M., Gray, W.M., Fassler, J.S. and Malone, R.E. Phylogenetic footprinting reveals multiple regulatory elements involved in control of the meiotic recombination gene, REC102. Yeast, 19(2). 99-114.
13. Kamvysselis, M., Patterson, N., Edrizzi, M., Birren, B. and Lander, E.S. submitted.
14. Keogh, R.S., Seoighe, C. and Wolfe, K.H. Evolution of gene order and chromosome number in Saccharomyces, Kluyveromyces and related fungi. Yeast, 14 (5). 443-457.
15. Lawrence, C.E., Altschul, S.F., Boguski, M.S., Liu, J.S., Neuwald, A.F. and Wootton, J.C. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262 (5131). 208-214.
16. Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., Zeitlinger, J., Jennings, E.G., Murray, H.L., Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J.B., Volkert, T.L., Fraenkel, E., Gifford, D.K. and Young, R.A. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science, 298 (5594). 799-804.
17. Liu, X., Brutlag, D.L. and Liu, J.S. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput. 127-138.
18. McCue, L., Thompson, W., Carmack, C., Ryan, M.P., Liu, J.S., Derbyshire, V. and Lawrence, C.E. Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res, 29 (3). 774-782.
19. Mewes, H.W., Frishman, D., Guldener, U., Mannhaupt, G., Mayer, K., Mokrejs, M., Morgenstern, B., Munsterkotter, M., Rudd, S. and Weil, B. MIPS: a database for genomes and protein sequences. Nucleic Acids Res, 30 (1). 31-34.
20. Roth, F.P., Hughes, J.D., Estep, P.W. and Church, G.M. Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol, 16 (10). 939-945.
21. Simon, I., Barnett, J., Hannett, N., Harbison, C.T., Rinaldi, N.J., Volkert, T.L., Wyrick, J.J., Zeitlinger, J., Gifford, D.K., Jaakkola, T.S. and Young, R.A. Serial regulation of transcriptional regulators in the yeast cell cycle. Cell, 106 (6). 697-708.
22. Tatusov, R.L., Koonin, E.V. and Lipman, D.J. A genomic perspective on protein families. Science, 278 (5338). 631-637.
23. Tatusov, R.L., Natale, D.A., Garkavtsev, I.V., Tatusova, T.A., Shankavaram, U.T., Rao, B.S., Kiryutin, B., Galperin, M.Y., Fedorova, N.D. and Koonin, E.V. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res, 29 (1). 22-28.
24. Tavazoie, S., Hughes, J.D., Campbell, M.J., Cho, R.J. and Church, G.M. Systematic determination of genetic network architecture. Nat Genet, 22 (3). 281-285.
25. Thompson, J.D., Higgins, D.G. and Gibson, T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res, 22 (22). 4673-4680.
26. Tompa, M. Identifying functional elements by comparative DNA sequence analysis. Genome Res, 11 (7). 1143-1144.
27. Wingender, E., Chen, X., Fricke, E., Geffers, R., Hehl, R., Liebich, I., Krull, M., Matys, V., Michael, H., Ohnhauser, R., Pruss, M., Schacherer, F., Thiele, S. and Urbach, S. The TRANSFAC system on gene expression regulation. Nucleic Acids Res, 29 (1). 281-283.
28. Zhang, M.Q. Promoter analysis of co-regulated genes in the yeast genome. Comput Chem, 23 (3-4). 233-250.
29. Zhu, J. and Zhang, M.Q. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15 (7-8). 607-611.