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Mutual information-based feature selection in studying perturbation of dendritic structure caused by TSC2 inactivation

Mutual information-based feature selection in studying perturbation of dendritic structure caused... In this study, the effect of protein Tuberous sclerosis 2 (TSC2) on the dendritic spine density and length was demonstrated by using TSC2-RNA inactivation. In addition, the role of rapamycin, an antagonist of the molecular target of rapamycin, in the morphological changes of spine caused by TSC2 silencing was investigated. The features were extracted from high-resolution three-dimensional image stacks collected by two-photon laser scanning microscopy of green fluorescing pyramidal cells expressing TSC2-RNA interference (RNAi), or TSC2-RNAi and rapamycin treatment in rat hippocampal slice cultures. We proposed to apply the lognormal distribution method for feature extraction. The extracted features of three cases under investigation, namely, (1) green-fluorescent protein GFP vs TSC2-RNAi, (2) GFP vs TSC2-RNAi and rapamycin, and (3) TSC2-RNAi vs TSC2-RNAi and rapamycin, were analyzed by mutual information-based feature selection and evaluated by three classifiers, K-nearest neighbor, Perceptron, and two-layer neural networks. The results showed that both the spine density and length have significant morphological changes after TSC2-RNAi treatment. However, rapamycin treatment could reverse the effect of TSC2-RNAi on spine length but not on spine density. These results are consistent with the results reported in the scientific literature. Finally, we explored the application of pattern recognition method in a small sample with richer feature properties, namely bootstrap mutual information estimation and a mutual information-based feature selection method. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Neuroinformatics Springer Journals

Mutual information-based feature selection in studying perturbation of dendritic structure caused by TSC2 inactivation

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Publisher
Springer Journals
Copyright
Copyright © 2006 by Humana Press Inc
Subject
Chemistry; Biotechnology; Engineering, general; Neurology
ISSN
1539-2791
eISSN
1559-0089
DOI
10.1385/NI:4:1:81
pmid
16595860
Publisher site
See Article on Publisher Site

Abstract

In this study, the effect of protein Tuberous sclerosis 2 (TSC2) on the dendritic spine density and length was demonstrated by using TSC2-RNA inactivation. In addition, the role of rapamycin, an antagonist of the molecular target of rapamycin, in the morphological changes of spine caused by TSC2 silencing was investigated. The features were extracted from high-resolution three-dimensional image stacks collected by two-photon laser scanning microscopy of green fluorescing pyramidal cells expressing TSC2-RNA interference (RNAi), or TSC2-RNAi and rapamycin treatment in rat hippocampal slice cultures. We proposed to apply the lognormal distribution method for feature extraction. The extracted features of three cases under investigation, namely, (1) green-fluorescent protein GFP vs TSC2-RNAi, (2) GFP vs TSC2-RNAi and rapamycin, and (3) TSC2-RNAi vs TSC2-RNAi and rapamycin, were analyzed by mutual information-based feature selection and evaluated by three classifiers, K-nearest neighbor, Perceptron, and two-layer neural networks. The results showed that both the spine density and length have significant morphological changes after TSC2-RNAi treatment. However, rapamycin treatment could reverse the effect of TSC2-RNAi on spine length but not on spine density. These results are consistent with the results reported in the scientific literature. Finally, we explored the application of pattern recognition method in a small sample with richer feature properties, namely bootstrap mutual information estimation and a mutual information-based feature selection method.

Journal

Neuroinformatics – Springer Journals

Published: Apr 11, 2007

References

  • Using mutual information for selecting features in supervised neural net learning
    Battiti, R.
  • Elements of Information Theory
    Cover, T. M.; Thomas, J. A.
  • Biostatistics: A Foundation For Analysis in the Health Sciences
    Daniel, W. W.
  • Photon upmanship: why multiphoton imaging is more than a gimmick
    Denk, W.; Svoboda, K.
  • Small sample issues for microarray-based classification
    Dougherty, E. R.
  • Pattern Classification
    Duda, R. O.; Hart, P. E.; Stork, D. G.
  • Reduced dendritic spinedensity on cerebral cortical pyramidal neurons in schizophrenia
    Garey, L. J.; Ong, W. Y.; Patel, T. S.
  • TSC2 is phosphorylated and inhibited by Akt and suppresses mTOR signaling
    Inoki, K.; Li, Y.; Zhu, T.; Wu, J.; Guan, K. L.
  • Abnormal dendritic spine characteristics in the temporal and visual cortices of patients with fragile-X syndrome: a quantitative examination
    Irwin, S. A.; Patel, B.; Idupulapati, M.; Harris, J. B.; Crisostomo, R. A.
  • An image analysis algorithm for dendritic spines
    Koh, I. Y.; Lindquist, W. B.; Zito, K.; Nimchinsky, E. A.; Svoboda, K.
  • Experience-dependent plasticity of dendritic spines in the developing rat barrel cortex in vivo
    Lendvai, B.; Stern, E. A.; Chen, B.; Svoboda, K.
  • Neuronal transfection in brain slices using particle-mediated gene transfer
    Lo, D. C.; McAllister, A. K.; Katz, L. C.
  • Abnormal dendritic patterns and aberrant spine development in Bourneville's disease—a Golgi survey
    Machado-Salas, J. P.
  • Pyramidal cell abnormalities in the motor cortex of a child with Down's syndrome, A Golgi Study
    Marin-Padilla, M.
  • TSC1-TSC2: a complex tale of PKB-mediated S6K regulation
    McManus, E. J.; Alessi, D. R.
  • An increase in dendritic spine density on hippocampal CA1 pyramidal cells following spatial learning in adult rats suggests the formation of new synapses
    Moser, M. B.; Trommald, M.; Anderson, P.
  • Structure and function of dendritic spines
    Nimchinsky, E. A.; Sabatini, B. L.; Svoboda, K.
  • Akt regulates growth by directly phosphorylating Tsc2
    Potter, C. J.; Pedraza, L. G.; Xu, T.
  • Adult fragile X syndrome. Cliniconeuropathologic findings
    Rudelli, R. D.; Brown, W. T.; Wisniewski, K.
  • A simple method for organotypic cultures of nervous tissue
    Stoppini, L.; Buchs, P. A.; Muller, D.
  • Regulation of neuronal morphology and function by the tumor suppressors TSC1 and TSC2
    Tavazoie, S. F.; Alvarez, V. A.; Ridenour, D. A.; Kwiatkowski, D. J.; Sabatini, B. L.
  • Missing value estimation methods for DNA microarrays
    Troyanskaya, O.; Cantor, M.; Sherlock, G.
  • Dendritic spines as basic functional units of neuronal integration
    Yuste, R.; Denk, W.
  • Binarization of microarray data based on a mixture model
    Zhou, X.; Wang, X.; Dougherty, E. R.
  • Missing value estimation based on linear and nonlinear regression with Bayesian gene selection
    Zhou, X.; Wang, X.; Dougherty, E. R.
  • Nonlinear-probit gene classification using mutual-information and wavelet based feature selection
    Zhou, X.; Wang, X.; Dougherty, E. R.
  • Towards automated cellular image segmentation for RNAi genome-wide screening
    Zhou, X.; Liu, K. L.; Bradley, P.; Perrimon, N.; Wong, S. T. C.
  • The bootstrap and its application in signal processing
    Zoubir, A. M.; Boashash, B.