gNCA: A framework for determining transcription factor activity based on transcriptome: Identifiability and numerical implementation

Metabolic Engineering

Volumn 7, Issue 2, 2005, Pages 128-141

  Tran, Linh M ^a   Brynildsen, Mark P ^a   Kao, Katy C ^a   Suen, Jason K ^a   Liao, James C ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

DNA microarray; Regulatory network; Transcription factor; Transcriptome

Indexed keywords

CARBON; GENES; MATHEMATICAL MODELS; NETWORK COMPONENTS; NUMERICAL ANALYSIS;

CARBON SOURCE TRANSITION; NETWORK COMPONENT ANALYSIS (NCA); SIGNAL DYNAMICS; TRANSCRIPTION NETWORK ANALYSIS;

ESCHERICHIA COLI;

TRANSCRIPTION FACTOR; TRANSCRIPTOME;

ARTICLE; BACTERIAL GENE; BACTERIAL STRAIN; CARBON SOURCE; CONTROLLED STUDY; DECOMPOSITION; DELETION MUTANT; DNA MICROARRAY; ESCHERICHIA COLI; KNOCKOUT GENE; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; NONHUMAN; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; STATISTICAL SIGNIFICANCE; THEORETICAL STUDY; TRANSCRIPTION INITIATION; WILD TYPE;

BACTERIAL OUTER MEMBRANE PROTEINS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; MODELS, BIOLOGICAL; REPRESSOR PROTEINS; TRANSCRIPTION, GENETIC;

ARCA; ESCHERICHIA COLI;

EID: 15244338624     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2004.12.001     Document Type: Article

References (24)

1. S. Alexeeva, K.J. Hellingwerf, and M.J.T. de Mattos Requirement of ArcA for redox regulation in E. coli under microaerobic but not anaerobic or aerobic conditions J. Bacteriol. 185 2003 204 209
2. J.S. Almeida, and E.O. Voit Neural-network-based parameter estimation in s-system models of biological networks Genome Inform. 14 2003 114 123
3. O. Alter, P.O. Brown, and D. Botstein Singular value decomposition for genome-wide expression data processing and modeling Proc. Natl. Acad. Sci. USA 97 2000 10101 10106
4. R.B. Bird, W.E. Stewart, and E.N. Lightfoot Transport Phenomena 2002 Wiley New York 895pp
5. D. Chang, D.J. Smalley, and T. Conway Gene expression profiling of E. coli growth transitions an expanded stringent response model Mol. Microbiol. 45 2002 289 306
6. H.C. Chen, H.C. Lee, T.Y. Lin, W.H. Li, and B.S. Chen Quantitative characterization of the transcriptional regulatory network in the yeast cell cycle Bioinformatics 20 2004 1914 1927
7. K.A. Datsenko, and B.L. Wanner One-step inactivation of chromosomal genes in E. coli K-12 using PCR Proc. Natl. Acad. Sci. USA 97 2000 6640 6645
8. P.C. Hansen, and D.P. O'Leary The use of the L-curve in the regularization of discrete ill-posed problems SIAM J. Sci. Comput. 14 1993 1487 1503
9. N.S. Holter, A. Maritan, M. Cieplak, N.V. Fedoroff, and J.R. Banavar Dynamic modeling of gene expression data Proc. Natl. Acad. Sci. USA 98 2001 1693 1698
10. S. Kalir, and U. Alon Using a quantitative blueprint to reprogram the dynamics of the flagella gene network Cell 117 2004 713 720
11. K.C. Kao, Y.L. Yang, R. Boscolo, C. Sabatti, V. Roychowdhury, and J.C. Lia Transcriptome-based determination of multiple transcription regulator activities in Escherichia coli by using network component analysis Proc. Natl. Acad. Sci. USA 101 2004 641 646
12. S.I. Lee, and S. Batzoglou Application of independent component analysis to microarrays Genome Biol. 4 2003 R76
13. T.I. Lee, N.J. Rinaldi, F. Robert, D.T. Odom, Z. Bar-Joseph, G.K. Geber, 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, and R.A. Yuong Transcriptional regulatory networks in Saccharomyces cerevisiae Science 298 2002 299 804
14. J.C. Liao, R. Boscolo, Y.L. Yang, L.M. Tran, C. Sabatti, and V. Roychowdhury Network component analysis reconstruction of regulatory signals in biological systems Proc. Natl. Acad. Sci. USA 100 2003 15522 15527
15. J.H. Miller A Short Course in Bacterial Genetics A Laboratory Manual and Handbook for E. coli and Related Bacteria 1992 Cold Spring Harbor Laboratory Press Cold Spring Harbor, NY
16. J. Misra, W. Shchmitt, D. Hwang, L.L. Hsiao, S. Gullans, G. Stephanopoulos, and G.N. Stephanopoulos Interactive exploration of microarray gene expression patterns in a reduced dimensional space Genome Res. 12 2002 1112 1120
17. S. Raychaudhuri, J.M. Stuart, and R.B. Altman Principal components analysis to summarize microarray experiments application to sporulation time series Proc. Symp. Biocomput. 5 2000 455 466
18. H. Salgado, A. Santos-Zavaleta, S. Gama-Castro, D. Millan-Zarate, E. Diaz-Peredo, F. Sanchez-Solano, E. Perez-Rueda, C. Bonavides-Martinez, and J. Collado-Vides RegulonDB (version 3.2) Transcriptional regulation and operon organization in E. coli K12 Nucl. Acids Res. 29 2001 72 74
19. M.A. Savageau Biochemical Systems Analysis A Study of Function and Design in Molecular Biology 1976 Addison-Wesley Reading, MA
20. G. Strang, and T. Nguyen Wavelets and Filter Banks 1997 Wellesley-Cambridge Press Cambridge
21. A.N. Tikhonov, and V.Y. Arsenin Solutions of Ill-Posed Problems 1977 Winston & Son Washington, DC
22. N.V. Torres, and E.O. Voit Pathway Analysis and Optimization in Metabolic Engineering 2002 Cambridge University Press New York
23. E.O. Voit, and J. Almeida Decoupling dynamical systems for pathway identification from metabolic profiles Bioinformatics 20 2004 1670 1681
24. M.K. Yeung, J. Tegner, and J.J. Collins Reverse engineering gene networks using singular value decomposition and robust regression Proc. Natl. Acad. Sci. USA 99 2002 6163 6168