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Network-based de-noising improves prediction from microarray data

2006

Article

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Prediction of human cell response to anti-cancer drugs (compounds) from microarray data is a challenging problem, due to the noise properties of microarrays as well as the high variance of living cell responses to drugs. Hence there is a strong need for more practical and robust methods than standard methods for real-value prediction. We devised an extended version of the off-subspace noise-reduction (de-noising) method to incorporate heterogeneous network data such as sequence similarity or protein-protein interactions into a single framework. Using that method, we first de-noise the gene expression data for training and test data and also the drug-response data for training data. Then we predict the unknown responses of each drug from the de-noised input data. For ascertaining whether de-noising improves prediction or not, we carry out 12-fold cross-validation for assessment of the prediction performance. We use the Pearson‘s correlation coefficient between the true and predicted respon se values as the prediction performance. De-noising improves the prediction performance for 65% of drugs. Furthermore, we found that this noise reduction method is robust and effective even when a large amount of artificial noise is added to the input data. We found that our extended off-subspace noise-reduction method combining heterogeneous biological data is successful and quite useful to improve prediction of human cell cancer drug responses from microarray data.

Author(s): Kato, T. and Murata, Y. and Miura, K. and Asai, K. and Horton, PB. and Tsuda, K. and Fujibuchi, W.
Journal: BMC Bioinformatics
Volume: 7
Number (issue): Suppl. 1
Pages: S4-S4
Year: 2006
Month: March
Day: 0

Department(s): Empirical Inference
Bibtex Type: Article (article)

Digital: 0
DOI: 10.1186/1471-2105-7-S1-S4
Language: en
Organization: Max-Planck-Gesellschaft
School: Biologische Kybernetik

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BibTex

@article{4071,
  title = {Network-based de-noising improves prediction from microarray data},
  author = {Kato, T. and Murata, Y. and Miura, K. and Asai, K. and Horton, PB. and Tsuda, K. and Fujibuchi, W.},
  journal = {BMC Bioinformatics},
  volume = {7},
  number = {Suppl. 1},
  pages = {S4-S4},
  organization = {Max-Planck-Gesellschaft},
  school = {Biologische Kybernetik},
  month = mar,
  year = {2006},
  month_numeric = {3}
}