Neuronal apoptosis revealed by genomic analysis: Integrating gene expression profiles with functional information

Neuroinformatics

Volumn 5, Issue 2, 2007, Pages 115-126

  Cavallaro, Sebastiano ^a  

^a INSTITUTE OF NEUROLOGICAL SCIENCES   (Italy)

Author keywords

Apoptosis; Cluster; Gene expression; Microarray; Neuron

Indexed keywords

THYROID HORMONE;

APOPTOSIS; COMPUTER PROGRAM; COMPUTER SYSTEM; DNA MICROARRAY; FATTY ACID METABOLISM; GENE CLUSTER; GENE EXPRESSION; GENETIC ANALYSIS; HORMONE METABOLISM; MEDICAL INFORMATION; NERVE CELL; PRIORITY JOURNAL; REVIEW; ANIMAL; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENETICS; GENOMICS; HUMAN; MICROARRAY ANALYSIS; PHYSIOLOGY;

ANIMALS; APOPTOSIS; CLUSTER ANALYSIS; GENE EXPRESSION PROFILING; GENOMICS; HUMANS; MICROARRAY ANALYSIS; NEURONS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS;

EID: 35148834244     PISSN: 15392791     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12021-007-0006-3     Document Type: Review

References (25)

1. Arends, M. J., & Wyllie, A. H. (1991). Apoptosis: Mechanisms and roles in pathology. International Review of Experimental Pathology, 32, 223-254.
2. Atlante, A., Bobba, A., Calissano, P., Passarella, S., & Marra, E. (2003). The apoptosis/necrosis transition in cerebellar granule cells depends on the mutual relationship of the antioxidant and the proteolytic systems which regulate ROS production and cytochrome c release en route to death. Journal of Neurochemistry, 84, 960-971.
3. Atlante, A., Gagliardi, S., Minervini, G. M., Marra, E., Passarella, S., & Calissano, P. (1996). Rapid uncoupling of oxidative phosphorylation accompanies glutamate toxicity in rat cerebellar granule cells. NeuroReport, 7, 2519-2523.
4. Borsello, T., Di Luzio, A., Ciotti, M. T., Calissano, P., & Galli, C. (2000). Granule neuron DNA damage following deafferentation in adult rats cerebellar cortex: A lesion model. Neuroscience, 95, 163-171.
5. Cavallaro, S., D'Agata, V., Alessi, E., Coffa, S., Alkon, D. L., Manickam, P., et al. (2004). Gene expression profiles of apoptotic neurons. Genomics, 84, 485-496.
6. D'Mello, S. R., & Chin, P. C. (2005). Treating neurodegenerative conditions through the understanding of neuronal apoptosis. Current Drug Targets. CNS. Neurology Disorders, 4, 3-23.
7. D'Mello, S. R., Galli, C., Ciotti, T., & Calissano, P. (1993). Induction of apoptosis in cerebellar granule neurons by low potassium: Inhibition of death by insulin-like growth factor I and cAMP. Proceedings of the National Academy of Sciences of the United States of America, 90, 10989-10993.
8. Eisen, M. B., Spellman, P. T., Brown, P. O., & Botstein, D. (1998). Cluster analysis and display of genome-wide expression patterns. Proceedings of the National Academy of Sciences of the United States of America, 95, 14863-14868.
9. Elvidge, G. (2006). Microarray expression technology: From start to finish. Pharmacogenomics, 7, 123-134.
10. Forgy, E. W. (1965). Cluster analysis of multivariate data: Efficiency vs interpretability of classifications. Biometrics, 21, 768-769.
11. Galli, C., Meucci, O., Scorziello, A., Werge, T. M., Calissano, P., & Schettini, G. (1995). Apoptosis in cerebellar granule cells is blocked by high KCl, forskolin, and IGF-1 through distinct mechanisms of action: The involvement of intracellular calcium and RNA synthesis. Journal of Neuroscience, 15, 1172-1179.
12. Heller, M. J. (2002). DNA microarray technology: Devices, systems, and applications. Annual Review of Biomedical Engineering, 4, 129-153.
13. Hess, K. R., Zhang, W., Baggerly, K. A., Stivers, D. N., & Coombes, K. R. (2001). Microarrays: Handling the deluge of data and extracting reliable information. Trends in Biotechnology, 19, 463-468.
14. Huang, Z. (1998). Extensions to the k-means algorithm for clustering large data sets with categorical values. Data Mining and Knowledge Discovery, 2, 283-304.
15. Jellinger, K. A. (2006). Challenges in neuronal apoptosis. Current Alzheimer Research, 3, 377-391.
16. Mattson, M. P. (2006). Neuronal life-and-death signaling, apoptosis, and neurodegenerative disorders. Antioxidants & Redox Signalling, 8, 1997-2006.
17. Noordewier, M. O., & Warren, P. V. (2001). Gene expression microarrays and the integration of biological knowledge. Trends in Biotechnology, 19, 412-415.
18. Paratore, S., Parenti, R., Torrisi, A., Copani, A., Cicirata, F., & Cavallaro, S. (2006). Genomic profiling of cortical neurons following exposure to beta-amyloid. Genomics, 88(4), 468-479.
19. Pettmann, B., & Henderson, C. E. (1998). Neuronal cell death. Neuron, 20, 633-647.
20. Sobek, J., Bartscherer, K., Jacob, A., Hoheisel, J. D., & Angenendt, P. (2006). Microarray technology as a universal tool for high-throughput analysis of biological systems. Combinatorial Chemistry & High Throughput Screening, 9, 365-380.
21. Sokal, R. R., & Michener, C. D. (1958). A statical method for evaluating systematic relationships. University of Kansas Science Bulletin, 38, 1409-1438.
22. Tompa, M., Li, N., Bailey, T. L., Church, G. M., De Moor, B., Eskin, E., et al. (2005). Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology, 23, 137-144.
23. Tryon, R. C. (1939). Cluster analysis. New York: McGraw-Hill.
24. Williams, R. W., & Herrup, K. (1988). The control of neuron number. Annual Review of Neuroscience, 11, 423-453.
25. Xiao, Q., & Nikodem, V. M. (1998). Apoptosis in the developing cerebellum of the thyroid hormone deficient rat. Front Bioscience, 3, A52-A57.