Transcriptional networks: reverse-engineering gene regulation on a global scale

被引:47
作者
Chua, G [1 ]
Robinson, MD [1 ]
Morris, Q [1 ]
Hughes, TR [1 ]
机构
[1] Univ Toronto, Banting & Best Dept Med Res, Toronto, ON M5G 1L6, Canada
基金
加拿大健康研究院; 加拿大自然科学与工程研究理事会;
关键词
D O I
10.1016/j.mib.2004.10.009
中图分类号
Q93 [微生物学];
学科分类号
071005 ; 100705 ;
摘要
A major objective in post-genome research is to fully understand the transcriptional control of each gene and the targets of each transcription factor. In yeast, large-scale experimental and computational approaches have been applied to identify co-regulated genes, cis regulatory elements, and transcription factor DNA binding sites in vivo. Methods for modeling and predicting system behavior, and for reconciling discrepancies among data types, are being explored. The results indicate that a complete and comprehensive yeast transcriptional network will ultimately be achieved.
引用
收藏
页码:638 / 646
页数:9
相关论文
共 53 条
[1]   Structure and evolution of transcriptional regulatory networks [J].
Babu, MM ;
Luscombe, NM ;
Aravind, L ;
Gerstein, M ;
Teichmann, SA .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 2004, 14 (03) :283-291
[2]   Identifying cooperativity among transcription factors controlling the cell cycle in yeast [J].
Banerjee, N ;
Zhang, MQ .
NUCLEIC ACIDS RESEARCH, 2003, 31 (23) :7024-7031
[3]   Functional genomics as applied to mapping transcription regulatory networks [J].
Banerjee, N ;
Zhang, MX .
CURRENT OPINION IN MICROBIOLOGY, 2002, 5 (03) :313-317
[4]   Computational discovery of gene modules and regulatory networks [J].
Bar-Joseph, Z ;
Gerber, GK ;
Lee, TI ;
Rinaldi, NJ ;
Yoo, JY ;
Robert, F ;
Gordon, DB ;
Fraenkel, E ;
Jaakkola, TS ;
Young, RA ;
Gifford, DK .
NATURE BIOTECHNOLOGY, 2003, 21 (11) :1337-1342
[5]   Predicting gene expression from sequence [J].
Beer, MA ;
Tavazoie, S .
CELL, 2004, 117 (02) :185-198
[6]   Additivity in protein-DNA interactions: how good an approximation is it? [J].
Benos, PV ;
Bulyk, ML ;
Stormo, GD .
NUCLEIC ACIDS RESEARCH, 2002, 30 (20) :4442-4451
[7]   FootPrinter: a program designed for phylogenetic footprinting [J].
Blanchette, M ;
Tompa, M .
NUCLEIC ACIDS RESEARCH, 2003, 31 (13) :3840-3842
[8]   Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors [J].
Bulyk, ML ;
Johnson, PLF ;
Church, GM .
NUCLEIC ACIDS RESEARCH, 2002, 30 (05) :1255-1261
[9]   Transcription factor binding element detection using functional clustering of mutant expression data [J].
Chen, GX ;
Hata, N ;
Zhang, MQ .
NUCLEIC ACIDS RESEARCH, 2004, 32 (08) :2362-2371
[10]   Phylogenetically and spatially conserved word pairs associated with gene-expression changes in yeasts [J].
Chiang, DY ;
Moses, AM ;
Kellis, M ;
Lander, ES ;
Eisen, MB .
GENOME BIOLOGY, 2003, 4 (07)