Reverse engineering of gene networks with LASSO and nonlinear basis functions

Annals of the New York Academy of Sciences

Volumn 1158, Issue , 2009, Pages 265-275

  Gustafsson, Mika ^a   Hörnquist, Michael ^a   Lundström, Jesper ^b   Björkegren, Johan ^b   Tegnér, Jesper ^a,b  

^a LINKÖPING UNIVERSITY   (Sweden)

^b KAROLINSKA UNIVERSITY HOSPITAL   (Sweden)

Author keywords

DREAM conference; LARS; LASSO; Network inference; Nonlinear; Reverse engineering

Indexed keywords

ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; GENE INTERACTION; GENETIC ALGORITHM; GENETIC ENGINEERING; GENETIC MODEL; MATHEMATICAL ANALYSIS; NONLINEAR SYSTEM; PERFORMANCE; SCORING SYSTEM;

EID: 63849175334     PISSN: 00778923     EISSN: 17496632     Source Type: Book Series    
DOI: 10.1111/j.1749-6632.2008.03764.x     Document Type: Article

References (22)

1. Tegnér, J. J. Björkegren. 2007. Perturbations to uncover gene networks. Trends Genet. 23 : 34 41.
2. Kauffman, S.A. 1969. Metabolic stability and epigenesis in randomly constructed genetic nets. Theor. Biol. 22 : 437 467.
3. Karlsson, F. M. Hörnquist. 2007. Order or chaos in Boolean gene networks depends on the mean fraction of canalizing functions. Phsyica A 384 : 747 757.
4. Werner, M., I. Ernberg, J. Zou, et al. 2007. Epstein-Barr virus latency switch in human B-cells : a physico-chemical model. BMC Syst. Biol. 1 : 40.
5. Margolin, A.A. A. Califano. 2007. Theory and limitations of genetic network inference from microarray data. Ann. N. Y. Acad. Sci. 1115 : 51 72.
6. D'haeseleer, P., X. Wen, S. Fuhrman R. Somogyi. 1999. Linear modeling of mRNA expression levels during CNS development and injury. In Pacific Symposium on Biocomputing, Vol. 4. R.B. Altman, A.K. Dunker, L. Hunter, et al., Eds 41 52. World Scientific Publishing Co. Singapore.
7. Gustafsson, M., M. Hörnquist A. Lombardi. 2005. Constructing and analyzing a large-scale gene-to-gene regulatory network-lasso-constrained inference and biological validation. IEEE/ACM Trans. Comput. Biol. Bioinform. 2 : 254 261.
8. Bansal, M., V. Belcastro, A. Ambesi-Impiombato D. di Bernardo. 2007. How to infer gene networks from expression profiles. Mol. Syst. Biol. 3 : 78.
9. Stolovitzky, G., D. Monroe A. Califano. 2007. Dialogue on reverse-engineering assessment and methods. The dream of high-throughput pathway inference. Ann. N. Y. Acad. Sci. 1115 : 1 22.
10. DREAM, Dialogue on Reverse-Engineering Assessment and Methods (2007), project webpage : http://wiki.c2b2.columbia.edu/dream/index.php/The-DREAM- Project.
11. Efron, B., T. Hastie, I. Johnstone R. Tibshirani. 2004. Least angle regression. Ann. Stat. 32 : 407 499.
12. Vanden Berghen, F. 2005. LARS Library: Least Angle Regression Stagewise Library. The MATLAB implementation is utilized here. Unpublished.
13. Tibshirani, R. 1996. Regression Shrinkage and selection via the Lasso. J. Roy. Stat. Soc., Ser. B 58 : 267 288.
14. Hoops, S., S. Sahle, R. Gauges, et al. 2006. COPASI - a complex pathway simulator. Bioinformatics 22 : 3067 3074.
15. Barabási, A.-L. Z. Oltvai. 2004. Network biology: Understanding the cell's functional organization. Nat. Rev. Genet. 5 : 101 113.
16. Gustafsson, M., M. Hörnquist A. Lombardi. 2006. Comparison and validation of community structures in complex networks. Physica A: Stat. Mech. Appl. 367 : 559 576.
17. Hartwell, L.H., J.J. Hopfield, S. Leibler A.W. Murray. 1999. From molecular to modular cell biology. Nature 402 : C47 C52.
18. Milo, R., S. Shen-Orr, S. Itzkovitz, et al. 2002. Network motifs: simple building blocks of complex networks. Science 298 : 824 827.
19. Gustafsson, M. M. Hörnquist. 2008. Integrating expression data, protein-protein interaction data and TF-binding data for improved quality in reverse engineering of gene regulatory networks. In Computational Methods in Gene Regulatory Networks. S. Das, D. Caragea, S. Welch & W. Hsu, Eds. IGI Global, Hershey, PA.
20. Nilsson, R., J.M. Peña, J. Björkegren J. Tegnér. 2007. Consistent feature selection for pattern recognition in polynomial time. J. Mach. Learn. Res. 8 : 589 612.
21. Rice, J.J., Y. Tu G. Stolovitzky. 2005. Reconstructing biological networks using conditional correlation analysis. Bioinformatics 21 : 765 773.
22. Basso, K., A.A. Margolin, G. Stolovitzky, et al. 2005. Reverse engineering of regulatory networks in human B cells. Nat. Genet. 37 : 382 390.