Nucleic Acids Research Advance Access originally published online on September 18, 2006
Nucleic Acids Research 2006 34(17):4925-4936; doi:10.1093/nar/gkl595
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Nucleic Acids Research, 2006, Vol. 34, No. 17 4925-4936
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
Computational Biology |
Computational analysis of tissue-specific combinatorial gene regulation: predicting interaction between transcription factors in human tissues
1 Wilmer Institute, Johns Hopkins University School of Medicine Maumenee Building 844, 600 N. Wolfe Street, Baltimore, MD 21287, USA 2 Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine Maumenee Building 844, 600 N. Wolfe Street, Baltimore, MD 21287, USA 3 Department of Neuroscience, Johns Hopkins University School of Medicine Maumenee Building 844, 600 N. Wolfe Street, Baltimore, MD 21287, USA 4 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine Maumenee Building 844, 600 N. Wolfe Street, Baltimore, MD 21287, USA
*To whom correspondence should be addressed. Tel: +1 443 287 3882; Fax: 1+ 410 502 5382; Email: jiang.qian{at}jhmi.edu
Received April 25, 2006. Revised July 13, 2006. Accepted August 1, 2006.
Tissue-specific gene expression is generally regulated by more than a single transcription factor (TF). Multiple TFs work in concert to achieve tissue specificity. In order to explore these complex TF interaction networks, we performed a large-scale analysis of TF interactions for 30 human tissues. We first identified tissue-specific genes for 30 tissues based on gene expression databases. We then evaluated the relationships between TFs using the relative position and co-occurrence of their binding sites in the promoters of tissue-specific genes. The predicted TF–TF interactions were validated by both known protein–protein interactions and co-expression of their target genes. We found that our predictions are enriched in known protein–protein interactions (>80 times that of random expectation). In addition, we found that the target genes show the highest co-expression in the tissue of interest. Our findings demonstrate that non-tissue specific TFs play a large role in regulation of tissue-specific genes. Furthermore, they show that individual TFs can contribute to tissue specificity in different tissues by interacting with distinct TF partners. Lastly, we identified several tissue-specific TF clusters that may play important roles in tissue-specific gene regulation.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  Y. Wang, X.-S. Zhang, and Y. Xia Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data Nucleic Acids Res., October 1, 2009; 37(18): 5943 - 5958. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. G. Roider, B. Lenhard, A. Kanhere, S. A. Haas, and M. Vingron CpG-depleted promoters harbor tissue-specific transcription factor binding signals--implications for motif overrepresentation analyses Nucleic Acids Res., October 1, 2009; 37(19): 6305 - 6315. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 B. Xiang, M. Yi, L. Wang, W. Liu, W. Zhang, J. Ouyang, Y. Peng, W. Li, M. Zhou, H. Liu, et al. Preparation of polyclonal antibody specific for NOR1 and detection of its expression pattern in human tissues and nasopharyngeal carcinoma Acta Biochim Biophys Sin, September 1, 2009; 41(9): 754 - 762. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 U. J. Pape, H. Klein, and M. Vingron Statistical detection of cooperative transcription factors with similarity adjustment Bioinformatics, August 15, 2009; 25(16): 2103 - 2109. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
F. Colecchia, D. Kottwitz, M. Wagner, C. V. Pfenninger, G. Thiel, I. Tamm, C. Peterson, and U. A. Nuber Tissue-specific regulatory network extractor (TS-REX): a database and software resource for the tissue and cell type-specific investigation of transcription factor-gene networks Nucleic Acids Res., June 1, 2009; 37(11): e82 - e82. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
H. G. Roider, T. Manke, S. O'Keeffe, M. Vingron, and S. A. Haas PASTAA: identifying transcription factors associated with sets of co-regulated genes Bioinformatics, February 15, 2009; 25(4): 435 - 442. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Yu, J. Lin, D. J. Zack, J. T. Mendell, and J. Qian Analysis of regulatory network topology reveals functionally distinct classes of microRNAs Nucleic Acids Res., November 1, 2008; 36(20): 6494 - 6503. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
J. Hu, H. Hu, and X. Li MOPAT: a graph-based method to predict recurrent cis-regulatory modules from known motifs Nucleic Acids Res., August 1, 2008; 36(13): 4488 - 4497. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
G. Tuteja, S. T. Jensen, P. White, and K. H. Kaestner Cis-regulatory modules in the mammalian liver: composition depends on strength of Foxa2 consensus site Nucleic Acids Res., July 1, 2008; 36(12): 4149 - 4157. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
X. Wang, J. Gu, M. Q. Zhang, and Y. Li Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species Bioinformatics, January 15, 2008; 24(2): 165 - 171. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Meir, R. Dror, X. Yu, J. Qian, I. Simon, J. Pe'er, and I. Chowers Molecular Characteristics of Liver Metastases from Uveal Melanoma Invest. Ophthalmol. Vis. Sci., November 1, 2007; 48(11): 4890 - 4896. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 K. Ogasawara, T. Terada, J.-i. Asaka, T. Katsura, and K.-i. Inui Hepatocyte nuclear factor-4{alpha} regulates the human organic anion transporter 1 gene in the kidney Am J Physiol Renal Physiol, June 1, 2007; 292(6): F1819 - F1826. [Abstract] [Full Text] [PDF]
|
|