Constructing logical models of gene regulatory networks by integrating transcription factor-DNA interactions with expression data: An entropy-based approach

Journal of Computational Biology

Volumn 19, Issue 1, 2012, Pages 30-41

  Karlebach, Guy ^a   Shamir, Ron ^a  

^a TEL AVIV UNIVERSITY   (Israel)

Author keywords

algorithms; computational molecular biology

Indexed keywords

DNA; TRANSCRIPTION FACTOR;

ALGORITHM; ANIMAL; ARTICLE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; COMPUTER SIMULATION; DNA MICROARRAY; ENTROPY; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENETICS; METABOLISM; METHODOLOGY; MOUSE; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DNA; ENTROPY; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; MICE; MODELS, GENETIC; MODELS, STATISTICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; TRANSCRIPTION FACTORS;

EID: 84855426653     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2011.0100     Document Type: Article

References (32)

1. Akutsu, T., and Miyano, S. 2001. Selecting informative genes for cancer classification using gene expression data. Proc. IEEE-EURASIP Workshop Nonlinear Signal Image Process. 3-6.
2. Akutsu, T., Tamura, T., and Horimoto, K. 2009. Completing networks using observed data. Algorithmic Learn. Theor. 126-140.
3. Akutsu, T., Miyano, S., and Kuhara, S. 1999. Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pac. Symp. Biocomput. 17-28.
4. Ben-Dor, A., Shamir, R., and Yakhini, Z. 1999. Clustering gene expression patterns. J. Comput. Biol. 6, 281-297.
5. Chickarmane, V., Troein, C., Nuber, U.A., et al. 2006. Transcriptional dynamics of the embryonic stem cell switch. PLoS Comput. Biol. 2, e123.
6. Cox, R.S., 3rd, Surette, M.G., and Elowitz, M.B. 2007. Programming gene expression with combinatorial promoters. Mol. Syst. Biol. 3, 145.
7. Dimitrova, E.S., Licona, M.P., McGee, J., et al. 2010. Discretization of time series data. J. Comput. Biol. 17, 853-868.
8. Glass, L., and Kauffman, S. 1973. The logical analysis of continuous, non-linear biochemical control networks. J. Theor. Biol. 39, 103-129.
9. Hashimoto, R., Dougherty, E., Brun, M., et al. 2003. Efficient selection of feature sets possessing high coefficients of determination based on incremental determinations. Signal Process. 83, 695-712.
10. Ivanova, N., Dobrin, R., Lu, R., et al. 2006. Dissecting self-renewal in stem cells with RNA interference. Nature 442, 533-538. (Pubitemid 44167907)
11. Karlebach, G., and Shamir, R. 2010. Minimally perturbing a gene regulatory network to avoid a disease phenotype: the glioma network as a test case. BMC Syst. Biol. 4, 15.
12. Karlebach, G., and Shamir, R. 2008. Modelling and analysis of gene regulatory networks. Nat. Rev. Mol. Cell Biol. 9, 770-780.
13. Karp, R. 1972. Reducibility Among Combinatorial Problems. Complexity of Computer Computations. 85-103.
14. Koyuturk, M., Szpankowski, W., and Grama, A. 2004. Biclustering gene-feature matrices for statistically significant dense patterns. Proc. IEEE Comput. Syst. Bioinformatics Conf. (CSB'04) 480-484. (Pubitemid 40276287)
15. Krzywinski, M., Schein, J., Birol, I., et al. 2009. Circos: an information aesthetic for comparative genomics. Genome Res. 19, 1639-1645.
16. Lähdesmäki, H., Shmulevich, I., and Yli-Harja. 2003. On learning gene regulatory networks under the Boolean network model. Machine Learn. 52, 147-167.
17. Liang, S., Fuhrman, S., and Somogyi, R. 1998. Reveal, a general reverse engineering algorithm for inference of genetic network architectures. Pac. Symp. Biocomput. 18-29.
18. Lopes, F.M., Martins, D.C., Jr., and Cesar, R.M., Jr. 2008. Feature selection environment for genomic applications. BMC Bioinform. 9, 451.
19. Lorenz, E.N. 1993. The Essence of Chaos. University of Washington Press, Seattle.
20. MacArthur, B., Ma'ayan, A., and Lemischka, I. 2009. Systems biology of stem cell fate and cellular reprogramming. Nat. Rev. Mol. Cell Biol. 10, 672-681.
21. Marson, A., Levine, S.S., Cole, M.F., et al. 2008. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134, 521-533.
22. Mayo, A.E., Setty, Y., Shavit, S., et al. 2006. Plasticity of the cis-regulatory input function of a gene. PLoS Biol. 4, e45.
23. Milo, R., Shen-Orr, S., Itzkovitz, S., et al. 2002. Network motifs: simple building blocks of complex networks. Science 298, 824-827. (Pubitemid 35231534)
24. Novershtern, N., Subramanian, A., Lawton, L.N., et al. 2011. Densely interconnected transcriptional circuits control cell states in human hematopoiesis. Cell 144, 296-309.
25. Saeys, Y., Inza, I., and Larranaga, P. 2007. A review of feature selection techniques in bioinformatics. Bioinformatics 23, 2507-2517. (Pubitemid 350048351)
26. Segal, E., Shapira, M., Regev, A., et al. 2003. Module networks: identifying regulatory modules and their conditionspecific regulators from gene expression data. Nat. Genet. 34, 166-176. (Pubitemid 36666927)
27. Shamir, R., and Tanay, A. 2003. Modeling transcription programs: inferring binding site activity and dose-response model optimization. Proc. RECOMB'03.
28. Thomas, R. 1973. Boolean formalization of genetic control circuits. J. Theor. Biol. 42, 563-585.
29. Tsong, A.E., Tuch, B.B., Li, H., et al. 2006. Evolution of alternative transcriptional circuits with identical logic. Nature 443, 415-420. (Pubitemid 44477273)
30. Ulitsky, I., Laurent, L.C., and Shamir, R. 2010. Towards computational prediction of microRNA function and activity. Nucleic Acids Res. 38, e160.
31. Xu, H., Schaniel, C., Lemischka, I.R., et al. 2010. Toward a complete in silico, multi-layered embryonic stem cell regulatory network. Wiley Interdiscip. Rev. Syst. Biol. Med. 2, 708-733.
32. Zhou, Q., Chipperfield, H., Melton, et al. 2007. A gene regulatory network in mouse embryonic stem cells. Proc. Natl. Acad. Sci. U.S.A. 104, 16438-16443. (Pubitemid 350211036)