Identifying tissue-selective transcription factor bindings sites in vertebrate promoters

被引:94
作者
Smith, AD
Sumazin, P
Zhang, MQ
机构
[1] Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA
[2] Portland State Univ, Dept Comp Sci, Portland, OR 97207 USA
关键词
bioinformatics; motif discovery;
D O I
10.1073/pnas.0406123102
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 computational method aimed at systematically identifying tissue-selective transcription factor binding sites. Our method focuses on the differences between sets of promoters that are associated with differentially expressed genes, and it is effective at identifying the highly degenerate motifs that characterize vertebrate transcription factor binding sites. Results on simulated data indicate that our method detects motifs with greater accuracy than the leading methods, and its detection of strongly overrepresented motifs is nearly perfect. We present motifs identified by our method as the most overrepresented in promoters of liver- and muscle-selective genes, demonstrating that our method accurately identifies known transcription factor binding sites and previously uncharacterized motifs.
引用
收藏
页码:1560 / 1565
页数:6
相关论文
共 28 条
[1]  
BAILEY TL, 1995, MACH LEARN, V21, P51, DOI 10.1007/BF00993379
[2]   Going the distance: A current view of enhancer action [J].
Blackwood, EM ;
Kadonaga, JT .
SCIENCE, 1998, 281 (5373) :60-63
[3]   Finding motifs using random projections [J].
Buhler, J ;
Tompa, M .
JOURNAL OF COMPUTATIONAL BIOLOGY, 2002, 9 (02) :225-242
[4]   EXPRESSION OF A SINGLE TRANSFECTED CDNA CONVERTS FIBROBLASTS TO MYOBLASTS [J].
DAVIS, RL ;
WEINTRAUB, H ;
LASSAR, AB .
CELL, 1987, 51 (06) :987-1000
[5]  
ESKIN E, 2004, RECOMB 04, P115
[6]   THE POU DOMAIN - VERSATILITY IN TRANSCRIPTIONAL REGULATION BY A FLEXIBLE 2-IN-ONE DNA-BINDING DOMAIN [J].
HERR, W ;
CLEARY, MA .
GENES & DEVELOPMENT, 1995, 9 (14) :1679-1693
[7]  
HERTZ GZ, 1990, COMPUT APPL BIOSCI, V6, P81
[8]   Mutation of hepatocyte nuclear factor-1β inhibits Pkhd1 gene expression and produces renal cysts in mice [J].
Hiesberger, T ;
Bai, Y ;
Shao, XL ;
McNally, BT ;
Sinclair, AM ;
Tian, X ;
Somlo, S ;
Igarashi, P .
JOURNAL OF CLINICAL INVESTIGATION, 2004, 113 (06) :814-825
[9]   A COMPILATION OF COMPOSITE REGULATORY ELEMENTS AFFECTING GENE-TRANSCRIPTION IN VERTEBRATES [J].
KEL, OV ;
ROMASCHENKO, AG ;
KEL, AE ;
WINGENDER, E ;
KOLCHANOV, NA .
NUCLEIC ACIDS RESEARCH, 1995, 23 (20) :4097-4103
[10]   Identity between rat htf and human xbp-1 genes:: determination of gene structure, target sequence, and transcription promotion function for HTF [J].
Kokura, K ;
Kishimoto, T ;
Tamura, T .
GENE, 2000, 241 (02) :297-307