Reverse engineering and analysis of genome-wide gene regulatory networks from gene expression profiles using high-performance computing

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 9, Issue 3, 2012, Pages 668-678

  Belcastro, Vincenzo ^a,b   Gregoretti, Francesco ^c   Siciliano, Velia ^a,b   Santoro, Michele ^a   D'Angelo, Giovanni ^a,b   Oliva, Gennaro ^c   Di Bernardo, Diego ^a,d  

^a TELETHON INSTITUTE OF GENETICS AND MEDICINE TIGEM   (Italy)

^b OPEN UNIVERSITY   (United Kingdom)

^c CNR   (Italy)

^d UNIVERSITY OF NAPLES FEDERICO II   (Italy)

Author keywords

Clustering algorithm; Gene regulatory network; Parallel computing; Reverse engineering

Indexed keywords

BIOLOGICAL FUNCTIONS; COMPUTATIONAL COSTS; GENE EXPRESSION PROFILES; GENE NETWORKS; GENE REGULATORY NETWORK; GENE REGULATORY NETWORKS; HIERARCHICAL CLUSTERING ALGORITHMS; HIGH-PERFORMANCE COMPUTING; INFERRED NETWORKS; MAMMALIAN CELLS; MEMORY REQUIREMENTS; MITOCHONDRIAL PROTEIN; MUS MUSCULUS; MUTUAL INFORMATIONS; NETWORK COMMUNITIES; PUBLIC REPOSITORIES; REGULATORY INTERACTIONS; REVERSE ENGINEERS; STATISTICAL EVIDENCE;

CLUSTERING ALGORITHMS; COMPUTER SOFTWARE SELECTION AND EVALUATION; ENGINEERS; PARALLEL ARCHITECTURES; PARALLEL PROCESSING SYSTEMS; REVERSE ENGINEERING;

GENE EXPRESSION;

MAMMALIA; MUS MUSCULUS;

MESSENGER RNA;

ALGORITHM; ANIMAL; ARTICLE; COMPUTER ANALYSIS; DNA MICROARRAY; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORK; GENOME; METABOLISM; METHODOLOGY; MOUSE;

ALGORITHMS; ANIMALS; COMPUTING METHODOLOGIES; GENE EXPRESSION PROFILING; GENE REGULATORY NETWORKS; GENOME; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; RNA, MESSENGER;

EID: 84859192845     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2011.60     Document Type: Article

References (21)

1. T.S. Gardner, D. di Bernardo, D. Lorenz, and J.J. Collins, "Inferring Genetic Networks and Identifying Compound Mode of Action via Expression Profiling," Science, vol. 301, no. 5629, pp. 102-105, 2003. (Pubitemid 36801571)
2. F. Gregoretti, V. Belcastro, D. di Bernardo, and G. Oliva, "A Parallel Implementation of the Network Identification by Multiple Regression (NIR) Algorithm to Reverse-Engineer Regulatory Gene Networks," PLoS One, vol. 5, no. 4, p. e10179, 2010, doi:10.1371/journal.pone.0010179.
3. Y. Yu, V.A. Smith, P.P. Wang, A.J. Hartemink, and E.D. Jarvis, "Advances to Bayesian Network Inference for Generating Causal Networks from Observational Biological Data," Bioinformatics, vol. 20, no. 18, pp. 3594-3603, 2004. (Pubitemid 40136795)
4. Margolin et al., "ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context," BMC Bioinformatics, vol. 7, Suppl. 1:S7, 2006, doi:10.1186/1471-2105-7-S1-S7. (Pubitemid 46437495)
5. Basso et al., "Reverse Engineering of Regulatory Networks in Human B Cells," Nature Genetics, vol. 37, no. 4, pp. 382-390, 2005.
6. M. Bansal, V. Belcastro, A. Ambesi-Impiombato, and D. di Bernardo, "How to Infer Gene Networks from Expression Profiles," Molecular Systems Biology, vol. 3, article no. 78, 2007, doi:10.1038/msb4100120.
7. A.J. Butte and I.S. Kohane, "Mutual Information Relevance Networks: Functional Genomic Clustering Using Pairwise Entropy Measurements," Proc. Pacific Symp. Biocomputing, pp. 418-429, 2000.
8. Prill et al., "Towards a Rigorous Assessment of Systems Biology Models: The Dream3 Challenges," PLoS One, vol. 5, no. 2, p. e9202, 2010, doi:10.1371/journal.pone.0009202.
9. H. Marcus, "Distribution of Mutual Information," Advanced in Neuronal Information Processing Systems, vol. 18, pp. 339-406, 2004.
10. B. Goebel, Z. Dawy, J. Hagenauer, and J.C. Mueller, "An Approximation to the Distribution of Finite Sample Size Mutual Information Estimates," Proc. IEEE Int'l Conf. Comm. (ICC), vol. 2, pp. 1102-1106, 2005. (Pubitemid 41259588)
11. E. Ravasz, A.L. Somera, D.A. Mongru, Z.N. Oltvai, and A.L. Barabsi, "Hierarchical Organization of Modularity in Metabolic Networks," Science, vol. 297, no. 5586, pp. 1551-1555, 2002. (Pubitemid 34971002)
12. Ravasi et al., "An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man," Cell, vol. 140, pp. 744-752, 2010.
13. G.N. Lance and W.T. Williams, "A General Theory of Classificatory Sorting Strategies: 1. Hierarchical Systems," The Computer J., vol. 9, no. 4, pp. 373-380, http://dx.doi.org/10.1093/comjnl/ 9.4.373, Feb. 1967.
14. R.R. Sokal and C.D. Michener, "A Statistical Method for Evaluating Systematic Relationships," Univ. of Kansas Scientific Bull., vol. 28, pp. 1409-1438, 1958.
15. P. Jaccard, " Etude Comparative De La Distribution Florale Dans Une Portion Des Alpes et Des Jura," Bull. Del La Société Vaudoise Des Sciences Naturelles, vol. 37, pp. 547-579, 1901.
16. Z. Du and F. Lin, "A Hierarchical Clustering Algorithm for MIMD Architecture," Computational Biology and Chemistry, vol. 28, nos. 5/ 6, pp. 417-419, http://www.sciencedirect.com/science/article/ B73G2-4DTKN09-1/2/ 029ee9da84343b63e8f432afae9d0fa0, 2004.
17. V. Belcastro, V. Siciliano, F. Gregoretti, P. Mithbaokar, G. Dharmalingam, S. Berlingieri, F. Iorio, G. Oliva, R. Polishchuck, N. Brunetti-Pierri, and D. di Bernardo, "Transcriptional Gene Network Inference from a Massive Dataset Elucidates Transcriptome Organization and Gene Function," Nucleic Acids Research, 2011, doi:10.1093/nar/gkr593.
18. S. Kim, S. Imoto, and S. Miyano, "Inferring Gene Networks from Time Series Microarray Data Using Dynamic Bayesian Networks," Briefings in Bioinformatics, vol. 4, no. 3, pp. 228-235, 2003.
19. W.K. Lim, K. Wang, C. Lefebvre, and A. Califano, "Comparative Analysis of Microarray Normalization Procedures: Effects on Reverse Engineering Gene Networks," Bioinformatics, vol. 23, no. 13, pp. i282-i288, 2007. (Pubitemid 47244411)
20. M. Ashburner, C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, J.T. Eppig, M.A. Harris, D.P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J.C. Matese, J.E. Richardson, M. Ringwald, G.M. Rubin, and G. Sherlock, "Gene Ontology: Tool for the Unification of Biology, the Gene Ontology Consortium," Nature Genetics, vol. 25, no. 1, pp. 25-29, http://dx.doi.org/10.1038/75556, May 2000. (Pubitemid 30257031)
21. P. Horton, K.-J. Park, T. Obayashi, N. Fujita, H. Harada, C.J. Adams-Collier, and K. Nakai, "WoLF PSORT: Protein Localization Predictor," Nucleic Acids Research, vol. 35, no. suppl. 2, pp. W585-W587, http://dx.doi.org/10.1093/nar/gkm259, July 2007.