Discovery of sequence motifs related to coexpression of genes using evolutionary computation

被引:68
作者
Fogel, GB
Weekes, DG
Varga, G
Dow, ER
Harlow, HB
Onyia, JE
Su, C
机构
[1] Nat Select Inc, La Jolla, CA 92037 USA
[2] Lilly Res Labs, Indianapolis, IN 46285 USA
关键词
D O I
10.1093/nar/gkh713
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Transcription factors are key regulatory elements that control gene expression. Recognition of transcription factor binding site (TFBS) motifs in the upstream region of coexpressed genes is therefore critical towards a true understanding of the regulations of gene expression. The task of discovering eukaryotic TFBSs remains a challenging problem. Here, we demonstrate that evolutionary computation can be used to search for TFBSs in upstream regions of genes known to be coexpressed. Evolutionary computation was used to search for TFBSs of genes regulated by octamer-binding factor and nuclear factor kappa B. The discovered binding sites included experimentally determined known binding motifs as well as lists of putative, previously unknown TFBSs. We believe that this method to search nucleotide sequence information efficiently for similar motifs will be useful for discovering TFBSs that affect gene regulation.
引用
收藏
页码:3826 / 3835
页数:10
相关论文
共 44 条
[1]  
Atteson K, 1998, Proc Int Conf Intell Syst Mol Biol, V6, P17
[2]  
Back T., 1997, Handbook of evolutionary computation
[3]  
Back T., 1996, Evolutionary Algorithms in Theory and Practice: Evolution Strategies, Evolutionary Programming, Genetic Algorithms
[4]  
BAILEY TL, 1995, MACH LEARN, V21, P51, DOI 10.1007/BF00993379
[5]   Gene expression data analysis [J].
Brazma, A ;
Vilo, J .
FEBS LETTERS, 2000, 480 (01) :17-24
[6]   Predicting gene regulatory elements in silico on a genomic scale [J].
Brazma, A ;
Jonassen, I ;
Vilo, J ;
Ukkonen, E .
GENOME RESEARCH, 1998, 8 (11) :1202-1215
[7]  
BREMMERMAN HJ, 1962, SELF ORG SYSTEMS
[8]   Regulatory elements and expression profiles [J].
Bucher, P .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 1999, 9 (03) :400-407
[9]  
Cantu-Paz E., 2000, EFFICIENT ACCURATE P
[10]   The transcriptional program of sporulation in budding yeast [J].
Chu, S ;
DeRisi, J ;
Eisen, M ;
Mulholland, J ;
Botstein, D ;
Brown, PO ;
Herskowitz, I .
SCIENCE, 1998, 282 (5389) :699-705