Improving gene network inference by comparing expression time-series across species, developmental stages or tissues

Journal of Bioinformatics and Computational Biology

Volumn 2, Issue 4, 2004, Pages 765-783

  Bourque, Guillaume ^a,c   Sankoff, David ^b  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b GENOME INSTITUTE OF SINGAPORE   (Singapore)

^c UNIVERSITY OF OTTAWA   (Canada)

Author keywords

Differential equations; Expression time series; Gene network inference; Multiple regression

Indexed keywords

ARTICLE; COMPUTER SIMULATION; DEVELOPMENTAL STAGE; GENE EXPRESSION PROFILING; GENE INTERACTION; GENETIC ANALYSIS; GENETIC REGULATION; HIPPOCAMPUS; LINEAR REGRESSION ANALYSIS; MATHEMATICAL ANALYSIS; NERVOUS SYSTEM DEVELOPMENT; NONHUMAN; QUALITY CONTROL; RAT; SPECIES DIFFERENCE; SPINAL CORD; TIME SERIES ANALYSIS;

ALGORITHMS; CELL PHYSIOLOGY; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; MODELS, BIOLOGICAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION; SPECIES SPECIFICITY; TIME FACTORS;

EID: 10944257452     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720004000892     Document Type: Article

References (31)

1. Lockhart DJ, Winzeler EA, Genomics, gene expression and DNA arrays, Nature 405(6788):827-836, 2000.
2. Schulze A, Downward J, Navigating gene expression using microarrays - a technology review, Nat Cell Biol 3(8):190-195, 2001.
3. DeRisi JL, Iyer VR, Brown PO, Exploring the metabolic and genetic control of gene expression on a genomic scale, Science 278 5338):680-686, 1997.
4. Spellman PT, Sherlock G, Zhang MQ, Iyer VR, Anders K, Eisen MB, Brown PO, Botstein D, Futcher B, Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization, Mol Biol Cell 9(12):3273-3297, 1998.
5. Roberts CJ, Nelson B, Marton MJ, Stoughton R, Meyer MR, Bennett HA, He YD, Dai H, Walker WL, Hughes TR, Tyers M, Boo C, Friend SH, Signaling and circuitry of multiple MAPK pathways revealed by a matrix of global gene expression profiles, Science 287(5454):873-880, 2000.
6. Quackenbush J, Genomics. microarrays - guilt by association, Science 302(5643): 240-241, 2003.
7. Akutsu T, Miyano S, Kuhara S, Identification of genetic networks from a small number of gene expression patterns under the Boolean network model, in Pac Symp Biocomput pp. 17-28, 1999.
8. Liang S, Fuhrman S, Somogyi R, Reveal, a general reverse engineering algorithm for inference of genetic network architectures, in Pac Symp Biocomput pp. 18-29, 1998.
9. Shmulevich I, Dougherty ER, Kim S, Zhang W, Probabilistic Boolean Networks: A rule-based uncertainty model for gene regulatory networks, Bioinformatics 18(2): 261-274, 2002.
10. Friedman N, Linial M, Nachman I, Pe'er D, Using Bayesian networks to analyze expression data, J Comput Biol 7(3-4):601-620, 2000.
11. Imoto S, Goto T, Miyano S, Estimation of genetic networks and functional structures between genes by using Bayesian networks and nonparametric regression, in Pac Symp Biocomput pp. 175-186, 2002.
12. Smith VA, Jarvis ED, Hartemink AJ, Evaluating functional network inference using simulations of complex biological systems, Bioinformatics 18(Suppl 1):216-224, 2002.
13. Ong IM, Glasner JD, Page D, Modelling regulatory pathways in E. coli from time series expression profiles, Bioinformatics 18 (Suppl 1):241-248, 2002.
14. Perrin BE, Ralaivola L, Mazurie A, Bottani S, Mallet J, D'Alche-Buc F, Gene networks inference using dynamic Bayesian networks, Bioinformatics 19(Suppl 2): II138-II148, 2003.
15. Husmeier D, Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks, Bioinformatics 19 (17):2271-2282, 2003.
16. Chen T, He HL, Church GM, Modeling gene expression with differential equations, Pac Symp Biocomput pp. 29-40, 1999.
17. D'Haeseleer P, Wen X, Fuhrman S, Somogyi R, Linear modeling of mRNA expression levels during CNS development and injury, in Pac Symp Biocomput pp. 41-52, 1999.
18. Wahde M, Hertz J, Coarse-grained reverse engineering of genetic regulatory networks, Biosystems 55(1-3):129-136, 2000.
19. Wahde M, Hertz J, Modeling genetic regulatory dynamics in neural development, J Comput Biol 8(4):429-442, 2001.
20. Weaver DC, Workman CT, Stormo GD, Modeling regulatory networks with weight matrices, in Pac Symp Biocomput pp. 112-123, 1999.
21. van Someren E, Wessels L, Reinders M, Genetic network models: A comparative study, in Proc. of SPIE 2001.
22. De Hoon M, Imoto S, Miyano S, Inferring gene regulatory networks from time-ordered gene expression data using differential equations, in Steffen Lange, Ken Satoh, and Carl H. Smith, (eds.), Fifth International Conference on Discovery Science, Lecture Notes in Computer Science 2534, pp. 267-274, Lbeck, Germany, Springer-Verlag, 2002.
23. van Someren EP, Wessels LFA, Reinders MJT, Information extraction for modeling gene expressions, in Biemond J, (ed.), 21st Symp. on Information Theory in the Benelux, pp. 215-222, Wassenaar (NL), 2000. Werkgemeenschap Informatieen Communicatietheorie, Enschede (NL).
24. van Someren EP, Wessels LFA, Reinders MJT, Backer E, Searching for limited connectivity in genetic network, in Proc. of ICSB 2001.
25. Yeung MKS, Tegner J, Collins JJ, Reverse engineering gene networks using singular value decomposition and robust regression, Proc Natl Acad Sci USA 99(9):6163-6168, 2002.
26. Holter NS, Maritan A, Cieplak M, Fedoroff NV, Banavar JR, Dynamic modeling of gene expression data, Proc Natl Acad Sci USA 98 4):1693-1698, 2001.
27. Holter NS, Mitra M, Maritan A, Cieplak M, Banavar JR, Fedoroff NV, Fundamental patterns underlying gene expression profiles: Simplicity from complexity, Proc Natl Acad Sci USA 97(15):8409-8414, 2000.
28. Hornquist M, Hertz J, Wahde M, Effective dimensionality of large-scale expression data using principal component analysis, Biosystems 65(2-3):147-156, 2002.
29. Gardner TS, di Bernardo D, Lorenz D, Collins JJ, Inferring genetic networks and identifying compound mode of action via expression profiling, Science 301(5629): 102-105, 2003.
30. Stuart JM, Segal E, Koller D, Kim SK, A gene-coexpression network for global discovery of conserved genetic modules, Science 302 5643):249-255, 2003.
31. Wen X, Fuhrman S, Michaels GS, Carr DB, Smith S, Barker JL, Somogyi R, Large-scale temporal gene expression mapping of central nervous system development, Proc Natl Acad Sci USA 95(1):334-339, 1998.