Identifying temporal gene networks using signal processing metrics on time-series gene expression data

A. Agrawal, A. Mittal

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Scopus citations

Abstract

A gene network refers to the knowledge of the activators and inhibitors of all genes. Genes themselves are believed to function as regulators of other genes. Most work done so far either ignores time delay in gene regulation or assumes that it is constant. We here propose the use of signal processing metrics like correlation techniques to find the gene interactions. Also, a post-processing stage is developed to remove false interactions among genes due to common parents, and dynamic correlation thresholds are used for selecting suitable correlation coefficients for constructing the gene network. The proposed Correlation Based Network Learning Algorithm (CBNL Algorithm) considers the multi time delay relationships among the genes, and therefore estimates the temporal gene network. The implementation of our method is done in MATLAB and experimental results on Saccharomyces cerevisiae expression data and comparison with other methods indicate the effectiveness of the method.

Original languageEnglish (US)
Title of host publicationProceedings - 3rd International Conference on Intelligent Sensing and Information Processing, ICISIP 2005
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages87-92
Number of pages6
ISBN (Electronic)0780395883, 9780780395886
DOIs
StatePublished - Jan 1 2005
Event3rd International Conference on Intelligent Sensing and Information Processing, ICISIP 2005 - Bangalore, India
Duration: Dec 14 2005Dec 17 2005

Publication series

NameProceedings - 3rd International Conference on Intelligent Sensing and Information Processing, ICISIP 2005

Other

Other3rd International Conference on Intelligent Sensing and Information Processing, ICISIP 2005
CountryIndia
CityBangalore
Period12/14/0512/17/05

Keywords

  • Bayesian methods
  • Bioinformatics
  • Biomedical signal processing
  • Delay effects
  • Gene expression
  • Genetics
  • Mathematical model
  • Robust stability
  • Signal processing
  • Signal processing algorithms

ASJC Scopus subject areas

  • Artificial Intelligence
  • Computer Networks and Communications
  • Signal Processing

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  • Cite this

    Agrawal, A., & Mittal, A. (2005). Identifying temporal gene networks using signal processing metrics on time-series gene expression data. In Proceedings - 3rd International Conference on Intelligent Sensing and Information Processing, ICISIP 2005 (pp. 87-92). [1619417] (Proceedings - 3rd International Conference on Intelligent Sensing and Information Processing, ICISIP 2005). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/ICISIP.2005.1619417