MANIA: A Gene Network Reverse Algorithm for Compounds Mode-of-Action and Genes Interactions Inference

Darong Lai; Hongtao Lu; Mario Lauria; Diego Bernardo; Christine Nardini

Complex Sciences. First International Conference, Complex 2009, Shanghai, China, February 23-25, 2009. Revised Papers, Part 1

Research Article

MANIA: A Gene Network Reverse Algorithm for Compounds Mode-of-Action and Genes Interactions Inference

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@INPROCEEDINGS{10.1007/978-3-642-02466-5_37,
    author={Darong Lai and Hongtao Lu and Mario Lauria and Diego Bernardo and Christine Nardini},
    title={MANIA: A Gene Network Reverse Algorithm for Compounds Mode-of-Action and Genes Interactions Inference},
    proceedings={Complex Sciences. First International Conference, Complex 2009, Shanghai, China, February 23-25, 2009. Revised Papers, Part 1},
    proceedings_a={COMPLEX PART 1},
    year={2012},
    month={5},
    keywords={gene network gene expression reverse engineering Ordinary Differential Equations (ODE) compound mode-of-action},
    doi={10.1007/978-3-642-02466-5_37}
}

Darong Lai
Hongtao Lu
Mario Lauria
Diego Bernardo
Christine Nardini
Year: 2012
MANIA: A Gene Network Reverse Algorithm for Compounds Mode-of-Action and Genes Interactions Inference
COMPLEX PART 1
Springer
DOI: 10.1007/978-3-642-02466-5_37

Darong Lai^,*, Hongtao Lu¹^,*, Mario Lauria²^,*, Diego Bernardo²^,*, Christine Nardini³^,*

1: Shanghai Jiao Tong University
2: TIGEM
3: CAS-MPG PICB

*Contact email: darong.lai@gmail.com, lu-ht@cs.sjtu.edu.cn, lauria@tigem.it, dibernardo@tigem.it, christine@picb.ac.cn

Abstract

Understanding the complexity of the cellular machinery represents a grand challenge in molecular biology. To contribute to the deconvolution of this complexity, a novel inference algorithm based on linear ordinary differential equations is proposed, based on high-throughput gene expression data. The algorithm can infer (i) gene-gene interactions from steady state expression profiles (ii) mode-of-action of the components that can trigger changes in the system. Results demonstrate that the proposed algorithm can identify information with high performances, thus overcoming the limitation of current algorithms that can infer reliably only one.

Keywords: gene network gene expression reverse engineering Ordinary Differential Equations (ODE) compound mode-of-action

Published: 2012-05-11

: http://dx.doi.org/10.1007/978-3-642-02466-5_37