Sampling motifs on phylogenetic trees

被引:36
作者
Li, XM [1 ]
Wong, WH [1 ]
机构
[1] Stanford Univ, Dept Stat, Stanford, CA 94305 USA
关键词
transcription factor binding sites; Gibbs sampler; substitution matrix;
D O I
10.1073/pnas.0501620102
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
We present a method to find motifs by simultaneously using the overrepresentation property and the evolutionary conservation property of motifs. This method is applicable to divergent species where alignment is unreliable, which overcomes a major limitation of the current methods. The method has been applied to search regulatory motifs in four yeast species based on ChIp-chip data in Saccharomyces cerevisiae and obtained 20% higher accuracy than the best current methods. We also discovered cis-regulatory elements that govern the tight regulation of ribosomal protein genes in two distantly related insects by using this method. These results demonstrate that our method will be useful for the extraction of regulatory signals in multiple genomes.
引用
收藏
页码:9481 / 9486
页数:6
相关论文
共 18 条
[1]  
Bailey T., 1994, P 2 INT C INT SYST M, P28
[2]   FootPrinter: a program designed for phylogenetic footprinting [J].
Blanchette, M ;
Tompa, M .
NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3840-3842
[3]   Finding functional features in Saccharomyces genomes by phylogenetic footprinting [J].
Cliften, P ;
Sudarsanam, P ;
Desikan, A ;
Fulton, L ;
Fulton, B ;
Majors, J ;
Waterston, R ;
Cohen, BA ;
Johnston, M .
SCIENCE, 2003, 301 (5629) :71-76
[4]   MAXIMUM LIKELIHOOD FROM INCOMPLETE DATA VIA EM ALGORITHM [J].
DEMPSTER, AP ;
LAIRD, NM ;
RUBIN, DB .
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-METHODOLOGICAL, 1977, 39 (01) :1-38
[5]  
Eskin Eleazar, 2002, Bioinformatics, V18 Suppl 1, pS354
[6]   A hidden Markov Model approach to variation among sites in rate of evolution [J].
Felsenstein, J ;
Churchill, GA .
MOLECULAR BIOLOGY AND EVOLUTION, 1996, 13 (01) :93-104
[7]   Discovery of conserved sequence patterns using a stochastic dictionary model [J].
Gupta, M ;
Liu, JS .
JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION, 2003, 98 (461) :55-66
[8]   Transcriptional regulatory code of a eukaryotic genome [J].
Harbison, CT ;
Gordon, DB ;
Lee, TI ;
Rinaldi, NJ ;
Macisaac, KD ;
Danford, TW ;
Hannett, NM ;
Tagne, JB ;
Reynolds, DB ;
Yoo, J ;
Jennings, EG ;
Zeitlinger, J ;
Pokholok, DK ;
Kellis, M ;
Rolfe, PA ;
Takusagawa, KT ;
Lander, ES ;
Gifford, DK ;
Fraenkel, E ;
Young, RA .
NATURE, 2004, 431 (7004) :99-104
[9]   Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae [J].
Hughes, JD ;
Estep, PW ;
Tavazoie, S ;
Church, GM .
JOURNAL OF MOLECULAR BIOLOGY, 2000, 296 (05) :1205-1214
[10]   DETECTING SUBTLE SEQUENCE SIGNALS - A GIBBS SAMPLING STRATEGY FOR MULTIPLE ALIGNMENT [J].
LAWRENCE, CE ;
ALTSCHUL, SF ;
BOGUSKI, MS ;
LIU, JS ;
NEUWALD, AF ;
WOOTTON, JC .
SCIENCE, 1993, 262 (5131) :208-214