Delayed and hidden variables interactions in gene regulatory networks

Mina Moradi Kordmahalleh, Mohammad Gorji Sefidmazgi, Abdollah Homaifar, Ali Karimoddini, Anthony Guiseppi-Elie, Joseph L. Graves

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

4 Scopus citations

Abstract

Reverse Engineering of Gene Regulatory Networks (GRN), i.e. Finding appropriate mathematical models to understand complex cellular systems, can be used in disease diagnosis, treatment, and drug design. There are fundamental gaps in the construction of GRN with regard to modeling of hidden/delayed interactions. Addressing these deficiencies is critical to understanding complex intracellular processes and enabling full use of the vast and ever-growing amount of available genomic data. Current modeling strategies either ignore or oversimplify time delays resulted from transcription and translation processes during gene expression. In addition, many research works do not account hidden variables such as transcription factors, repressors, small metabolites, DNA, microRNA species that regulate themselves and other genes but are not readily detectable on micro array experiments. To capture the effect of these parameters, in this paper, we utilize our developed Partially Connected Artificial Neural Networks with Evolvable Topology (PANNET) to find a more comprehensive model of GRN by considering the effects of unknown hidden variables and different time delays. This method is innovative, since the structure of the network has memory and internal states, which can model the unknown hidden variables and time delays. We furthermore use a new evolutionary optimization based on variable-length Genetic Algorithm (GA) to find a sparse structure of PANNET to predict the gene expression levels accurately. Finally we demonstrate the capability of PANNET in constructing GRN, including the effect of different delays and unknown hidden variables through modeling of E. Coli SOS inducible DNA repair system.

Original languageEnglish (US)
Title of host publicationProceedings - IEEE 14th International Conference on Bioinformatics and Bioengineering, BIBE 2014
EditorsReda Alhajj, Taghi M. Khoshgoftaar, Nikolaos G. Bourbakis, Xingquan Zhu
PublisherInstitute of Electrical and Electronics Engineers Inc.
Pages23-29
Number of pages7
ISBN (Electronic)9781479975013
DOIs
StatePublished - Feb 5 2014
Event14th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2014 - Boca Raton, United States
Duration: Nov 10 2014Nov 12 2014

Publication series

NameProceedings - IEEE 14th International Conference on Bioinformatics and Bioengineering, BIBE 2014

Other

Other14th IEEE International Conference on BioInformatics and BioEngineering, BIBE 2014
CountryUnited States
CityBoca Raton
Period11/10/1411/12/14

Keywords

  • Artificial neural network genetic algorithm
  • Evolvable topology
  • Gene regulatory network
  • Time series

ASJC Scopus subject areas

  • Bioengineering
  • Biomedical Engineering

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