Article |
CRSD: a comprehensive web server for composite regulatory signature discovery
1 Department of Computer Science, National Chung-Hsing University Taichung, Taiwan, ROC 2 Institutes of Biomedical Sciences and Molecular Biology, National Chung-Hsing University Taichung, Taiwan, ROC 3 Graduate Institute of Epidemiology, National Taiwan University Taipei, Taiwan, ROC 4 Departments of Biotechnology and Bioinformatics, Asia University Taichung, Taiwan, ROC, 5 NTU Center for Genomic Medicine, National Taiwan University College of Medicine Taipei, Taiwan, ROC
*To whom correspondence should be addressed. Tel: 886 4 22840485, ext. 226; Fax: 886 4 22853469; Email: jwchen{at}dragon.nchu.edu.tw
Received February 14, 2006. Revised March 19, 2006. Accepted April 4, 2006.
Transcription factors (TFs) and microRNAs play important roles in the regulation of human gene expression, and the study of their combinatory regulations of gene expression is a new research field. We constructed a comprehensive web server, the composite regulatory signature database (CRSD), that can be applied in investigating complex regulatory behaviors involving gene expression signatures (GESs), microRNA regulatory signatures (MRSs) and TF regulatory signatures (TRSs). Six well-known and large-scale databases, including the human UniGene, mature microRNAs, putative promoter, TRANSFAC, pathway and Gene Ontology (GO) databases, were integrated to provide the comprehensive analysis in CRSD. Two new genome-wide databases, of MRSs and TRSs, were also constructed and further integrated into CRSD. To accomplish the microarray data analysis at one go, several methods, including microarray data pretreatment, statistical and clustering analysis, iterative enrichment analysis and motif discovery, were closely integrated in the web server, which has not been the case in previous studies. Our implementation showed that the published literature could demonstrate the results of genome-wide enrichment analysis. We conclude that CRSD is a powerful and useful bioinformatic web server and may provide new insights into gene regulation networks. CRSD and the online tutorial are publicly available at http://biochip.nchu.edu.tw/crsd1/.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C.-Y. Lee, H.-F. Sher, H.-W. Chen, C.-C. Liu, C.-H. Chen, C.-S. Lin, P.-C. Yang, H.-S. Tsay, and J. J.W. Chen Anticancer effects of tanshinone I in human non-small cell lung cancer Mol. Cancer Ther., November 1, 2008; 7(11): 3527 - 3538. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Novershtern, Z. Itzhaki, O. Manor, N. Friedman, and N. Kaminski A Functional and Regulatory Map of Asthma Am. J. Respir. Cell Mol. Biol., March 1, 2008; 38(3): 324 - 336. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 C. Backes, A. Keller, J. Kuentzer, B. Kneissl, N. Comtesse, Y. A. Elnakady, R. Muller, E. Meese, and H.-P. Lenhof GeneTrail--advanced gene set enrichment analysis Nucleic Acids Res., July 13, 2007; 35(suppl_2): W186 - W192. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
I. J. Donaldson and B. Gottgens CoMoDis: composite motif discovery in mammalian genomes Nucleic Acids Res., January 12, 2007; 35(1): e1 - e1. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C.-C. Liu, W.-S. E. Chen, C.-C. Lin, H.-C. Liu, H.-Y. Chen, P.-C. Yang, P.-C. Chang, and J. J.W. Chen Topology-based cancer classification and related pathway mining using microarray data Nucleic Acids Res., September 1, 2006; 34(14): 4069 - 4080. [Abstract] [Full Text] [PDF]
|
|