\begin{thebibliography}{99} \bibitem{}% T. Akutsu, S. Miyano, S. Kuhara, ``Identification of genetic networks from a small number of gene expression patterns under the Boolean network model'', The Pacific Symposium on Biocomputing, 4: 17-28, 1999. \bibitem{}% T. Akutsu, S. Miyano, S. Kuhara, ``Inferring qualitative relations in genetic networks and metabolic pathways'', Bioinformatics, 16(8): 727-734, 2000. \bibitem{}% Z. Bar-Joseph, G.K. Gerber, T.I. Lee, N.J. Rinaldi, J.Y. Yoo, F. Robert, D.B. Gordon, E. Fraenkel, T.S. Jaakkola, R.A. Young, D.K. Gifford, ``Computational discovery of gene modules and regulatory networks'', Nature Biotechnology, 21(11): 1337-1342, 2003. \bibitem{}% H.J. Bussemaker, H. Li, E.D. Siggia, ``Regulatory element detection using correlation with expression'', Nature Genetics, 27(2): 167-171, 2001. \bibitem{}% J.S. Buzas, T.D. Tosteson, L.A. Stefanski, Measurement Error, Institute of Statistics Mimeo Series No. 2544, 2003. \bibitem{}% M. Carey, S.T. Smale, Transcriptional Regulation in Eukaryotes, Cold Spring Harbor Laboratory Press, 1999. \bibitem{}% R.J. Carroll, ``Measurement error in epidemiologic studies'', in Encyclopedia of Biostatistics 2491-2519, 1998. \bibitem{}% S. Chu, J. DeRisi, M. Eisen, J. Mulholland, D. Botstein, P.O. Brown, I. Herskowitz, ``The transcriptional program of sporulation in budding yeast'', Science, 282(5389): 699-705, 1998. \bibitem{}% E.H. Davidson, J.P. Rast, P. Oliveri, A. Ransick, C. Calestani, C.H. Yuh, T. Minokawa, G. Amore, V. Hinman, C. Arenas-Mena, O. Otim, C.T. Brown, C.B. Livi, P.Y. Lee, R. Revilla, A.G. Rust, Z. Pan, M.J. Schilstra, P.J. Clarke, M.I. Arnone, L. Rowen, R.A. Cameron, D.R. McClay, L. Hood, H. Bolouri, ``A genomic regulatory network for development'', Science, 295(5560): 1669-78, 2002. \bibitem{}% H. de Jong, ``Modeling and simulation of genetic regulatory systems: a literature review'', Journal of Computational Biology, 9(1): 67-103, 2002. \bibitem{}% M.B. Eisen, P.T. Spellman, P.O. Brown, D. Botstein, ``Cluster analysis and display of genome-wide expression patterns'', Proceedings of the National Academy of Sciences USA, 95(25): 14863-14868, 1998. \bibitem{}% N. Friedman, M. Linial, I. Nachman, D. Pe'er, ``Using Bayesian networks to analyze expression data'', Journal of Computational Biology, 7(3-4): 601-620, 2000. \bibitem{}% W.A. Fuller, Measurement Error Models, Wiley, New York, 1987. \bibitem{}% F. Gao, B.C. Foat, H.J. Bussemaker HJ, ``Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data'', BioMed Central Bioinformatics. 5(1): 31, 2004. \bibitem{}% T.S. Gardner, D. di Bernardo, D. Lorenz, J.J. Collins JJ, ``Inferring genetic networks and identifying compound mode of action via expression profiling'', Science, 301(5629):102-105, 2003. \bibitem{}% A.J. Hartemink, D.K. Gifford, T.S. Jaakkola, R.A. Young, ``Using graphical models and genomic expression data to statistically validate models of genetic regulatory networks'', The Pacific Symposium on Biocomputing, 6: 422-33, 2001. \bibitem{}% A.J. Hartemink, D.K. Gifford, T.S. Jaakkola, R.A. Young, ``Combining location and expression data for principled discovery of genetic regulatory network models'', The Pacific Symposium on Biocomputing, 7: 437-49, 2002. \bibitem{}% T.I. Lee, N.J. Rinaldi, F. Robert, D.T. Odom, Z. Bar-Joseph, G.K. Gerber, N.M. Hannett, C.T. Harbison, C.M. Thompson, I. Simon, J. Zeitlinger, E.G. Jennings, H.L. Murray, D.B. Gordon, B. Ren, J.J. Wyrick, J.B. Tagne, T.L. Volkert, E. Fraenkel, D.K. Gifford, R.A. Young RA, ``ranscriptional regulatory networks in Saccharomyces cerevisiae'', Science, 298(5594): 799-804, 2002. \bibitem{}% S. Liang, S. Fuhrman, R. Somogyi R, ``Reveal, a general reverse engineering algorithm for inference of genetic network architectures'', The Pacific Symposium on Biocomputing, 3: 18-29, 1998. \bibitem{}% J.C. Liao, R. Boscolo, Y.L. Yang, L.M. Tran, C. Sabatti, V.P. Roychowdhury VP, ``Network component analysis: reconstruction of regulatory signals in biological systems'', Proceedings of the National Academy of Sciences USA, 100(26): 15522-15527, 2003. \bibitem{}% X.S. Liu, D.L. Brutlag, J.S. Liu JS, ``An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments'', Nature Biotechnology, 20(8): 835-839, 2002. \bibitem{}% B. Ren, F. Robert, J.J. Wyrick, O. Aparicio, E.G. Jennings, I. Simon, J. Zeitlinger, J. Schreiber, N. Hannett, E. Kanin, T.L. Volkert, C.J. Wilson, S.P. Bell, R.A. Young RA, ``Genome-wide location and function of DNA binding proteins'', Science, 290(5500): 2306-2309, 2000. \bibitem{}% S. Richardson, ``Measurent error modelling from a Bayesian perspective'', Bulletin of the International Statistical Institute, 1999. \bibitem{}% S. Richardson, and W.R. Gilks, ``Conditional independence models for epidemiological studies with covariate measurement error'', Statistics in Medicine, 12: 1703-1722, 1993. \bibitem{}% C.J. Roberts, B. Nelson, M.J. Marton, R. Stoughton, M.R. Meyer, H.A. Bennett, Y.D. He, H. Dai, W.L. Walker, T.R. Hughes, M. Tyers, C. Boone, S.H. Friend, ``Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles'', Science, 287(5454): 873-880, 2000. \bibitem{}% I. Shmulevich, E.R. Dougherty, S. Kim, W. Zhang, ``Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks'', Bioinformatics, 18(2): 261-274, 2002. \bibitem{}% P.T. Spellman, G. Sherlock, M.Q. Zhang, V.R. Iyer, K. Anders, M.B. Eisen, P.O. Brown, D. Botstein, B. Futcher, ``Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization'', Molecular Biology of the Cell, 9(12): 3273-3297, 1998. \bibitem{}% N. Sun, H. Zhao, ``Genomic approaches in dissecting complex biological pathways'', Pharmacogenomics, 5(2): 163-179, 2004. \bibitem{}% J. Tegnér, M.K. Yeung, J. Hasty, J.J. Collins, ``Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling'', Proceedings of the National Academy of Sciences USA, 100(10): 5944-5949, 2003. \bibitem{}% W. Wang, J.M. Cherry, D. Botstein, H. Li, ``A systematic approach to reconstructing transcription networks in Saccharomycescerevisiae'', Proceedings of the National Academy of Sciences USA, 99(26): 16893-16898, 2002. \bibitem{}% H. Zhao, B. Wu, N. Sun, ``DNA-Protein binding and gene expression patterns'', Science and Statistics: A festschrift for Terry Speed, Institutue of Mathematical Statistics Lecture Notes-Monograph Series, Vol 40:259-274, 2003. \bibitem{}% Z. Zhang, M. Gerstein, ``Reconstructing genetic networks in yeast'', Nature Biotechnology, 21(11): 1295-1297, 2003. \end{thebibliography}