The Community for Technology Leaders
RSS Icon
Issue No.02 - March-April (2013 vol.10)
pp: 393-400
Camilla Bernardini , Inst. of Anatomy & Cell Biol., Univ. Cattolica del Sacro Cuore, Rome, Italy
Federica Censi , Dept. of Technol. & Health, Ist. Superiore di Sanita, Rome, Italy
Wanda Lattanzi , Inst. of Anatomy & Cell Biol., Univ. Cattolica del Sacro Cuore, Rome, Italy
Giovanni Calcagnini , Dept. of Technol. & Health, Ist. Superiore di Sanita, Rome, Italy
Alessandro Giuliani , Dept. of Environ. & Health, Ist. Superiore di Sanita, Rome, Italy
The aim of this study was to analyze previously published gene expression data of skeletal muscle biopsies of Duchenne muscular dystrophy (DMD) patients and controls (gene expression omnibus database, accession #GSE6011) using systems biology approaches. We applied an unsupervised method to discriminate patient and control populations, based on principal component analysis, using the gene expressions as units and patients as variables. The genes having the highest absolute scores in the discrimination between the groups, were then analyzed in terms of gene expression networks, on the basis of their mutual correlation in the two groups. The correlation network structures suggest two different modes of gene regulation in the two groups, reminiscent of important aspects of DMD pathogenesis.
Muscular dystrophy, Genetics, Principal component analysis,gene regulation networks, principal component analysis, Duchenne muscular dystrophy
Camilla Bernardini, Federica Censi, Wanda Lattanzi, Giovanni Calcagnini, Alessandro Giuliani, "Gene Regulation Networks in Early Phase of Duchenne Muscular Dystrophy", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, no. 2, pp. 393-400, March-April 2013, doi:10.1109/TCBB.2013.24
[1] Y.W. Chen, P. Zhao, R. Borup, and E.P. Hoffman, "Expression Profiling in the Muscular Dystrophies: Identification of Novel Aspects of Molecular Pathophysiology," J. Cell Biology, vol. 151, no. 6, pp. 1321-1336, 2000.
[2] Y.W. Chen et al., "Early Onset of Inflammation and Later Involvement of TGFbeta in Duchenne Muscular Dystrophy," Neurology, vol. 65, no. 6, pp. 826-834, 2005.
[3] M. Pescatori et al., "Gene Expression Profiling in the Early Phases of DMD: A Constant Molecular Signature Characterizes DMD Muscle from Early Postnatal Life throughout Disease Progression," Federation of Am. Soc. for Experimental Biology, vol. 21, no. 4, pp. 1210-1226, 2007.
[4] S. Noguchi et al., "cDNA Microarray Analysis of Individual Duchenne Muscular Dystrophy Patients," Human Molecular Genetics, vol. 12, no. 6, pp. 595-600, 2003.
[5] J.N. Haslett et al., "Gene Expression Comparison of Biopsies from Duchenne Muscular Dystrophy (DMD) and Normal Skeletal Muscle," Proc Nat'l Academy of Sciences USA, vol. 99, no. 23, pp. 15000-15005, 2002.
[6] D. Noble, "Genes and Causation," Philosophical Trans. Series A Math. Physical Eng. Science, vol. 366, no. 1878, pp. 3001-3015, 2008.
[7] C. Romualdi et al., "Correlation between Gene Expression and Clinical Data through Linear and Nonlinear Principal Components Analyses: Muscular Dystrophies as Case Studies," OMICS, vol. 13, no. 3, pp. 173-184, June 2009.
[8] J.C. Roden et al., "Mining Gene Expression Data by Interpreting Principal Components," BMC Bioinformatics, vol. 7, article 194, 2006.
[9] S. Huang, "Reprogramming Cell Fates: Reconciling Rarity with Robustness," Bioessays, vol. 31, no. 5, pp. 546-560, 2009.
[10] A. Giuliani, "Collective Motions and Specific Effectors: A Statistical Mechanics Perspective on Biological Regulation," BMC Genomics, vol. 11, no. suppl 1, article S2, 2010.
[11] R.A. Irizarry et al., "Summaries of Affymetrix GeneChip Probe Level Data," Nucleic Acids Research, vol. 31, p. e15, 2003.
[12] A.L. Barabási and Z.N. Oltvai, "Network Biology: Understanding the Cell's Functional Organization," Nat'l Rev. Genetics, vol. 5, no. 2, pp. 101-113, 2004.
[13] G.A. Churchill and R.W. Doerge, "Empirical Threshold Values for Quantitative Trait Mapping," Genetics, vol. 138, no. 3, pp. 963-971, 1994.
[14] S. Huang, "Reprogramming Cell Fates: Reconciling Rarity with Robustness," Bioessays, vol. 31, pp. 546-560, 2009.
[15] D.A. Carrino, J.M. Sorrell, and A.I. Caplan, "Dynamic Expression of Proteoglycans during Chicken Skeletal Muscle Development and Maturation," Poultry Science, vol. 78, pp. 769-777, 1999.
[16] S. Ying et al., "Characterization and Expression of the Mouse Lumican Gene," J. Biology Chemistry, vol. 272, pp. 30306-30313, 1997.
[17] M. Dolhnikoff, J. Morin, P.J. Roughley, and M.S. Ludig, "Expression of Lumican in Human Lungs," Am. J. Respiratory Cell and Molecular Biology, vol. 19, pp. 582-587, 1998.
[18] F. Wu and S. Chakravarti, "Differential Expression of Inflammatory and Fibrogenic Genes and Their Regulation by NF-kappaB Inhibition in a Mouse Model of Chronic Colitis," J. Immunology, vol. 179, no. 10, pp. 6988-7000, 2007.
[19] F. Censi, A. Giuliani, P. Bartolini, and G. Calcagnini, "A Multiscale Graph Theoretical Approach to Gene Regulation Networks: A Case Study in Atrial Fibrillation," IEEE Trans. Biomedical Eng., vol. 58, no. 10, pp. 2943-2946, Oct. 2011.
[20] O. Alter, "Discovery of Principles of Nature from Mathematical Modeling of DNA Microarray Data," Proc. Nat'l Academy of Sciences USA, vol. 103, no. 44, pp. 16063-16064, Oct. 2006.
[21] D. Baron et al., "Meta-Analysis of Muscle Transcriptome Data Using the MADMuscle Database Reveals Biologically Relevant Gene Patterns," BMC Genomics, vol. 12, article 113, 2011.
[22] L.F. Li et al., "Lumican Expression in Diaphragm Induced by Mechanical Ventilation," PLoS One, vol. 6, no. 9, article e24692, 2011.
[23] A.P. Sjöberg et al., "Short Leucine-Rich Glycoproteins of the Extracellular Matrix Display Diverse Patterns of Complement Interaction and Activation," Molecular Immunology, vol. 46, no. 5, pp. 830-839, 2009.
[24] A. Kesari et al., "Dysferlin Deficiency Shows Compensatory Induction of Rab27A/Slp2a That May Contribute to Inflammatory Onset," Am. J. Pathology, vol. 173, no. 5, pp. 1476-1487, 2008.
[25] P.J. Murray and T.A. Wynn, "Protective and Pathogenic Functions of Macrophage Subsets," Nat'l Rev. Immunology, vol. 11, no. 11, pp. 723-737, 2011.
81 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool