An Efficient Convex Nonnegative Network Component Analysis for Gene Regulatory Network Reconstruction

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5780 LNBI, Issue , 2009, Pages 56-66

  Dai, Jisheng ^a   Chang, Chunqi ^a   Ye, Zhongfu ^b   Hung, Yeung Sam ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Convex programming; Gene regulatory network; Microarray; Network component analysis; Positivity constraints

Indexed keywords

COMPUTATIONAL COSTS; CONNECTIVITY MATRIX; CONVEX APPROACH; CONVEX PROGRAMMING; EXISTING METHOD; GENE EXPRESSION MICROARRAY; GENE REGULATORY NETWORK; GENE REGULATORY NETWORKS; NETWORK COMPONENT ANALYSIS; POSITIVITY CONSTRAINTS; REASONABLE ACCURACY; SIMULATION RESULT; SYSTEMS BIOLOGY;

BIOINFORMATICS; BIOLOGY; GENE EXPRESSION; PATTERN RECOGNITION;

NETWORK COMPONENTS;

EID: 70349871612     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-04031-3_6     Document Type: Conference Paper

References (19)

1. Friedman, N., Linial, M., Nachman, I., Peer, D.: Using bayesian networks to analyze expression data. Journal of Computational Biology 7(3), 601-620 (2000) (Pubitemid 30944025)
2. Shmulevich, I., Dougherty, E.R., Kim, S., Zhang, W.: Probabilistic boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinformatics 18(2), 261-274 (2002) (Pubitemid 34183104)
3. Dougherty, E.R., Shmulevich, I., Chen, J., Wang, Z.J.: Genomic Signal Processing and Statistics. Hindawi Publishing Corporation (2005)
4. Alter, O., Brown, P.O.: Singular value decomposition for genome-wide expression data processing and modeling. Proceedings of the National Academy of Sciences of the United States of America 97(18), 10101-10106 (2000)
5. Lee, S.I., Batzoglou, S.: Application of independent component analysis to microarrays. Genome Biology 4(11), R76 (2003)
6. Liao, J.C., Boscolo, R., Yang, Y.L., Tran, L.M., Sabatti, C., Roychowdhury, V.P.: Network component analysis: Reconstruction of regulatory signals in biological systems. Proceedings of the National Academy of Sciences of the United States of America 100(26), 15522-15527 (2003)
7. Chang, C.Q., Hung, Y.S., Fung, P.C.W., Ding, Z.: Network component analysis for blind source separation. In: Proc. 2006 International Conference on Communications, Circuits and Systems, Guilin, China, pp. 323-326 (2006)
8. Chang, C.Q., Ding, Z., Hung, Y.S., Fung, P.C.W.: Fast network component analysis for gene regulation networks. In: Proc. 2007 IEEE International Workshop on Machine Learning for Signal Processing, Thesaloniki, Greece, pp. 21-26 (2007)
9. Lee, T.I., Rinaldi, N.J., Robert, F., Odom, D.T., Bar-Joseph, Z., Gerber, G.K., Hannett, N.M., Harbison, C.T., Thompson, C.M., Simon, I., Zeitlinger, J., Jennings, E.G., Murray, H.L., Gordon, D.B., Ren, B., Wyrick, J.J., Tagne, J.B., Volkert, T.L., Fraenkel, E., Gi.ord, D.K., Young, R.A.: Transcriptional regulatory networks in saccharomyces cerevisiae. Science 298(5594), 799-804 (2002)
10. Wang, C., Xuan, J., Chen, L., Zhao, P., Wang, Y., Clarke, R., Ho.man, E.: Motifdirected network component analysis for regulatory network inference. BMC Bioinformatics 9(suppl. 1), S21 (2008)
11. Chang, C.Q., Ding, Z., Hung, Y.S., Fung, P.C.W.: Fast network component analysis (FastNCA) for gene regulatory network reconstruction from microarray data. Bioinformatics 24(11), 1349-1358 (2008)
12. Chang, C.Q., Ding, Z., Hung, Y.S.: A new optimization algorithm for network component analysis based on convex programming. In: Proc. 2009 IEEE International Conference on Acoustics, Speech and Signal Processing, Taipei, Taiwan (2009)
13. Chang, C.Q., Ding, Z., Hung, Y.S.: Nonnegative network component analysis by linear programming for gene regulatory network reconstruction. In: Adali, T., et al. (eds.) ICA 2009. LNCS, vol.5441, pp. 395-402. Springer, Heidelberg (2009)
14. Savageau, M.A.: Biochemical Systems Analysis: A Study of Function and Design in Molecular Biology. Addison-Wesley, Reading (1976)
15. Alon, U.: An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman & Hall/CRC, Boca Raton (2007)
16. Boyd, S., Vandenberghe, L.: Convex Optimization. Cambridge University Press, Cambridge (2004)
17. Golub, G.H., van Loan, C.F.: Matrix Computation, 3rd edn. The Johns Hopkins University Press (1996)
18. Lay, D.C.: Linear Algebra and Its Applications, 2nd edn. Addison-Wesley, New York (2000)
19. Spellman, P.T., Sherlock, G., Zhang, M.Q., Iyer, V.R., Anders, K., Eisen, M.B., Brown, P.O., Botsein, D., Futcher, B.: Comprehensive identification of cell cycleregulated genes of the yeast saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 9(12), 3273-3297 (1998)