Improved reconstruction of in silico gene regulatory networks by integrating knockout and perturbation data

PLoS ONE

Volumn 5, Issue 1, 2010, Pages

  Yip, Kevin Y ^a   Alexander, Roger P ^b   Yan, Koon Kiu ^b   Gerstein, Mark ^a,b  

^a Yale University   (United States)

^b YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALSENILIN;

ARTICLE; COMPUTER MODEL; GENE CONTROL; GENE DELETION; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; KNOCKOUT GENE; NOISE; PREDICTION; SIGNAL NOISE RATIO; GENE SILENCING; REGULATOR GENE; THEORETICAL MODEL;

GENE KNOCKDOWN TECHNIQUES; GENES, REGULATOR; MODELS, THEORETICAL;

EID: 77749264188     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0008121     Document Type: Article

References (23)

1. Bonneau R, Reiss DJ, Shannon P, Facciotti M, Hood L, et al. (2006) The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biology 7.
2. Gardner TS, di Bernardo D, Lorenz D, Collins JJ (2003) Inferring genetic networks and identifying compound mode of action via expression profiling. Science 301: 102-205.
3. Mendes P, Sha W, Ye K (2003) Artificial gene networks for objective comparison of analysis algorithms. Bioinformatics 19: ii122-ii129.
4. Vu TT, Vohradsky J (2007) Nonlinear differential equation model for quantification of transcriptional regulation applied to microarray data of Saccharomyces cerevisiae. Nucleic Acids Research 35: 279-287.
5. Cohen AA, Geva-Zatorsky N, Eden E, Frenkel-Morgenstern M, Issaeva I, et al. (2008) Dynamic proteomics of individual cancer cells in response to a drug. Science 322: 1511-1516.
6. Giaever G, Chu AM, Ni L, Connelly C, Riles L, et al. (2002) Functional profiling of the saccharomyces cerevisiae genome. Nature 418: 387-391.
7. Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, et al. (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421: 231-237.
8. Pe'er D, Regev A, Elidan G, Friedman N (2001) Inferring subnetworks from perturbed expression profiles. Bioinformatics 17: S215-S224.
9. Yeang CH, Ideker T, Jaakkola T (2004) Physical network models. Journal of Computational Biology 11: 243-262.
10. Vaske CJ, House C, Luu T, Frank B, Yeang CH, et al. (2009) A factor graph nested effects model to identify networks from genetic perturbations. PLoS Computational Biology 5.
11. Markowetz F, Kostka D, Troyanskaya OG, Spang R (2007) Nested effects models for high-dimensional phenotyping screens. Bioinformatics 23: i305-i312.
12. The DREAM (dialogue for reverse engineering assessments and methods) project. Available: http://wiki.c2b2.columbia.edu/dream/index.php/Main-Page.
13. Stolovitzky G, Prill RJ, Califano A (2009) Lessons from the DREAM2 challenges: A community effort to assess biological network inference. Annals of the New York Academy of Sciences 1158: 159-195.
14. Stolovitzky G, Monroe D, Califano A (2007) Dialogue on reverse-engineering assessment and methods: The DREAM of high-throughput pathway inference. Annals of the New York Academy of Sciences 1115: 1-22.
15. Wagner A (2004) Reconstructing pathways in large genetic networks from genetic perturbations. Journal of Computational Biology 11: 53-60.
16. Rice JJ, Tu Y, Stolovitzky G (2004) Reconstructing biological networks using conditional correlation analysis. Bioinformatics 21: 765-773.
17. Boyd S, Vandenberghe L (2004) Convex Optimization Cambridge University Press.
18. Dahlquist G, Björck A ° (2003) Numerical Methods. Dover.
19. The DREAM3 challenges. Available: http://wiki.c2b2.columbia.edu/dream/ index.php/The-DREAM3-Challenges.
20. Marbach D, Schaffter T, Mattiussi C, Floreano D (2009) Generating realistic in silico gene networks for performance assessment of reverse engineering methods. Journal of Computational Biology 16: 229-239.
21. Hughes TR, Marton MJ, Jones AR, Roberts CJ, Stoughton R, et al. (2000) Functional discovery via a compendium of expression profiles. Cell 102: 109-126.
22. Hu Z, Killion PJ, Iyer VR (2007) Genetic reconstruction of a functional transcriptional regulatory network. Nature Genetics 39: 683-687.
23. Chapelle O, Schölkopf B, Zien A, eds (2006) Semi-Supervised Learning. MIT Press.