Bioinformatics pp 379-392

Part of the Methods in Molecular Biology™ book series (MIMB, volume 453)

Genetic Signatures for a Rodent Model of Parkinson's Disease Using Combinatorial Optimization Methods

  • Mou'ath Hourani
  • Regina Berretta
  • Alexandre Mendes
  • Pablo Moscato

Abstract

This chapter illustrates the use of the combinatorial optimization models presented in Chapter 19 for the Feature Set selection and Gene Ordering problems to find genetic signatures for diseases using micro-array data. We demonstrate the quality of this approach by using a microarray dataset from a mouse model of Parkinson's disease. The results are accompanied by a description of the currently known molecular functions and biological processes of the genes in the signatures.

Key words:

Parkinson's disease combinatorial optimization gene selection microarray data analysis feature selection gene ordering 

References

  1. 1.
    Feany, M. (2004) New genetic insights into Parkinson's disease. NEJM 351, 1937–1940.PubMedCrossRefGoogle Scholar
  2. 2.
    Brown, V., Ossadtchi, A., Khan, A., et al. (2002) Multiplex three-dimensional brain gene expression mapping in a mouse model of Parkinson's disease. Genome Res 12, 868–884.PubMedGoogle Scholar
  3. 3.
    Cotta, C., Sloper, C., Moscato, P. (2004) Evolutionary search of thresholds for robust feature selection: application to microarray data, in EvoBIO2004. Proceedings of the 2nd European Workshop in Evolutionary Computation and Bioinformatics, in (Raidl, G., et al., eds.), Lecture Notes in Computer Science 3005, 31–40.Google Scholar
  4. 4.
    Moscato, P., Berretta, R., Hourani, M., et al. (2005a) Genes related with Alzheimer's disease: a comparison of evolutionary search, statistical and integer programming approaches, in EvoBIO2005. Proceedings of the 3rd European Workshop on Evolutionary Bioinformatics, in (Rothlauf, F., et al., eds.), Lecture Notes in Computer Science 3449, 84–94.Google Scholar
  5. 5.
    Berretta, R., Mendes, A., Moscato, P. (2005) Integer programming models and algorithms for molecular classification of cancer from microarray data. ACSC2005: Proceedings of the 28th Australasian Computer Science Conference, in (Estivill-Castro, V., ed.), Conferences in Research and Practice in Information Technology 38, 361–370.Google Scholar
  6. 6.
    Cotta, C., Langston, M., Moscato, P. (2006) Combinatorial and algorithmic issues for microarray data analysis, in (Gonzalez, T., ed.), Handbook of Approximation Algorithms and Metaheuristics. Chapman & Hall/CRC, Boca Raton, FL.Google Scholar
  7. 7.
    Moscato, P., Mathieson, L., Mendes, A., et al. (2005b) The electronic primaries: Predicting the U.S. presidency using feature selection with safe data reduction. ACSC2005: Proceedings of the 28th Australasian Computer Science Conference, in (Estivill-Castro, V., ed.), Conferences in Research and Practice in Information Technology 38, 371–380.Google Scholar
  8. 8.
    Kim, H., Golub, G., Park, H. (2004) Missing value estimation for DNA microarray gene expression data: local least squares imputation. Bioinformatics 21, 187–198.PubMedCrossRefGoogle Scholar
  9. 9.
    Lee, G., Tanaka, M., Park, K., et al. (2004) Casein kinase II-mediated phosphoryla-tion regulates alpha-synuclein/synphilin-1 interaction and inclusion body formation. J Biol Chem 279, 6834–6839.PubMedCrossRefGoogle Scholar
  10. 10.
    Chen, G., Bower, K. A., Ma, C., et al. (2004) Glycogen synthase kinase 3beta (GSK3beta) mediates 6-hydroxydopamine-induced neuronal death. FASEB J 18, 1162–1164.PubMedCrossRefGoogle Scholar
  11. 11.
    Bibbiani, F., Oh, J. D., Kielaite, A., et al. (2005) Combined blockade of AMPA and NMDA glutamate receptors reduces levodopa-induced motor complications in animal models of PD. Exp Neurol 196, 422–429.PubMedCrossRefGoogle Scholar
  12. 12.
    Uemura, K., Kuzuya, A., Shimohama, S. (2004) Protein trafficking and Alzheimer's disease. Curr Alzheimer Res 1, 1–10.PubMedCrossRefGoogle Scholar
  13. 13.
    Corso, T. D., Torres, G., Goulah, C., et al. (2005) Transfection of tyrosine kinase deleted FGF receptor-1 into rat brain sub-stantia nigra reduces the number of tyro-sine hydroxylase expressing neurons and decreases concentration levels of striatal dopamine. Mol Brain Res 139, 361–366.PubMedCrossRefGoogle Scholar
  14. 14.
    Jacobs, W., Walsh, G., Miller, F. (2004) Neuronal survival and p73/p63/p53: a family affair. Neuroscientist 10, 443–455.PubMedCrossRefGoogle Scholar
  15. 15.
    Albert, I., Gulgoni, C., Hakansson, K., et al. (2005) Increased D1 dopamine receptor signaling in levodopa-induced dyskinesia. Ann Neurol 57, 17–26.CrossRefGoogle Scholar
  16. 16.
    Widner, B., Leblhuber, F., Fuchs, D. (2002) Increased neopterin production and tryp-tophan degradation in advanced Parkinson's disease. J Neural Trans 109, 181–189.CrossRefGoogle Scholar
  17. 17.
    Wolff, J., Fisher, LJ., Xu, L., et al. (1989) Grafting fibroblasts genetically modified to produce L-dopa in a rat model of Parkinson disease. Proc Natl Acad Sci U S A 86, 9011–9014.PubMedCrossRefGoogle Scholar
  18. 18.
    Shi, J., Zhang, S., Tang, M., et al. (2004) Possible association between Cys311Ser polymorphism of paraoxonase 2 gene and late-onset Alzheimer's disease in Chinese. Mol Brain Res 120, 201–204.PubMedCrossRefGoogle Scholar
  19. 19.
    D'Adamo P., Menegon, A., Lo Nigro, C., et al. (1998) Mutations in GDI1 are responsible for X-linked non-specific mental retardation. Nat Genet 19, 134–139.PubMedCrossRefGoogle Scholar
  20. 20.
    Kolsch, H., Heun, R. (2003) Polymorphisms in genes of proteins involved in cholesterol metabolism: evidence for Alzheimer's disease? Neurobiol Lipids 2, 5–7.Google Scholar
  21. 21.
    Mattson, M. (2004) Metal-catalyzed disruption of membrane protein and lipid signaling in the pathogenesis of neurodegenerative disorders. Ann NY Acad Sci 1012, 37–50.PubMedCrossRefGoogle Scholar
  22. 22.
    Francisconi, S., Codenotti, M., Ferrari-Toninelli, G., et al. (2005) Preservation of DNA integrity and neuronal degeneration. Brain Res Rev 48, 347–351.PubMedCrossRefGoogle Scholar
  23. 23.
    Raina, A., Zhu, X., Rottkamp, C., et al. (2000) Cyclin toward dementia: cell cycle abnormalities and abortive oncogenesis in Alzheimer disease. J Neurosci Res 61, 128–133.PubMedCrossRefGoogle Scholar
  24. 24.
    Ogawa, O., Lee, H., Zhu, X., et al. (2003) Increased p27, an essential component of cell cycle control, in Alzheimer's disease. Aging Cell 2, 105–110.PubMedCrossRefGoogle Scholar
  25. 25.
    Lovell, M., Xie, C., Xiong, S., et al. (2003) Wilms' tumor suppressor (WT1) is a mediator of neuronal degeneration associated with the pathogenesis of Alzheimer's disease. Brain Res 983, 84–96.PubMedCrossRefGoogle Scholar
  26. 26.
    Czlonkowska, A., Kurkowska-Jastrzebska, I., Czlonkowski, A., et al. (2002) Immune processes in the pathogenesis of Parkinson's disease: a potential role for microglia and nitric oxide. Med Sci Mon 8, RA165–RA177.Google Scholar
  27. 27.
    Gainetdinov, R., Premont, R., Bohn, L., et al. (2004) Desensitization of G protein-coupled receptors and neuronal functions. Annu Rev Neurosci 27, 107–144.PubMedCrossRefGoogle Scholar
  28. 28.
    Magnoni, M., Govoni, S., Battaini, F., et al. (1991) The aging brain: protein phosphorylation as a target of changes in neuronal function. Life Sci 48, 373–385.PubMedCrossRefGoogle Scholar
  29. 29.
    Chase, T., Oh, J. (2000) Striatal mechanisms and pathogenesis of parkinsonian signs and motor complications. Ann Neu-rol 47, S122–S129.Google Scholar
  30. 30.
    Nicholson, D., Thornberry, N. (2003) Apoptosis: life and death decisions. Science 299, 214–215.PubMedCrossRefGoogle Scholar
  31. 31.
    Lindholma, D., Eriksson, O., Korhonen, L. (2004) Mitochondrial proteins in neuronal degeneration. Biochem Biophys Res Commun 321, 753–758.CrossRefGoogle Scholar
  32. 32.
    Takeda, S., Yamazaki, H., Seog, D., et al. (2000) Kinesin superfamily protein 3 (kif3) motor transports fodrin-associating vesicles important for neurite building. J Cell Biol 148, 1255–1266.PubMedCrossRefGoogle Scholar
  33. 33.
    Cheng, K., Li, Z., Fu, W., et al. (2002) Pctaire1 interacts with p35 and is a novel substrate for Cdk5/p35. J Biol Chem 277, 31988–31993.PubMedCrossRefGoogle Scholar
  34. 34.
    Robertson, L., Moya, K., Breen, K. (2004) The potential role of tau protein O-glyco-sylation in Alzheimer's disease. J Alzheimer's Dis 6, 489–495.Google Scholar
  35. 35.
    Bhatt, R., Tomoda, T., Fang, Y., et al. (2000) Discoidin domain receptor 1 functions in axon extension of cerebellar granule neurons. Gene Dev 14, 2216–2228.PubMedCrossRefGoogle Scholar
  36. 36.
    Ongusaha, P., Kim, J., Fang, L., et al. (2003) p53 induction and activation of DDR1 kinase counteract p53-mediated apoptosis and influence p53 regulation through a positive feedback loop. EMBO J 22, 1289–1301.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Mou'ath Hourani
    • 1
  • Regina Berretta
    • 2
  • Alexandre Mendes
    • 2
  • Pablo Moscato
    • 3
  1. 1.Newcastle Bioinformatics Initiative, School of Electrical Engineering and Computer ScienceThe University of NewcastleCallaghanAustralia
  2. 2.Centre of Bioinformatics, Biomarker Discovery and Information-Based MedicineThe University of NewcastleCallaghanAustralia
  3. 3.ARC Centre of Excellence in Bioinformatics, and Centre of Bioinformatics, Biomarker Discovery and Information-Based MedicineThe University of NewcastleCallaghanAustralia

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