article · 2003

Physical Network Models and Multi-source Data Integration

Chen-Hsiang Yeang And, Chen-hsiang Yeang, Tommi Jaakkola

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Abstract

We develop a new framework for inferring models of transcriptional regulation. The models in this approach, which we call physical models, are constructed on the basis of verifiable molecular attributes of the underlying biological system. The attributes include, for example, the existence of protein-protein and protein-DNA interactions in gene regulatory processes, the directionality of signal transduction in protein-protein interactions, as well as the signs of the immediate e#ects of these interactions (e.g., whether an upstream gen activates or represses the downstream genes). Each attribute is included as a variable in the model, and the variables define a collection of annotated random graphs. Possible configurations of these variables (realizations of the underlying biological system) are constrained by the available data sources. Some of the data sources such as factor-binding data (location data) involve measurements that are directly tied to the variables in the model. Other sources such as gene knock-outs are functional in nature and provide only indirect evidence about the (physical) variables. We associate each knock-out e#ect in the deletion mutant data with a set of causal paths (molecular cascades) that could in principle explain the e#ect, resulting in aggregate constraints about the physical variables in the model. The most likely setting of all the variables is found by the max-product algorithm.

Cite this paper

APA 7

And, C.-H. Y., Yeang, C.-H., & Jaakkola, T. (2003). Physical Network Models and Multi-source Data Integration.

MLA 9

And, Chen-Hsiang Yeang, et al. “Physical Network Models and Multi-source Data Integration.” 2003.

Chicago

And, Chen-Hsiang Yeang, Chen-hsiang Yeang, and Tommi Jaakkola. 2003. “Physical Network Models and Multi-source Data Integration.”

Harvard

And, C.-H.Y., Yeang, C.-H. and Jaakkola, T. (2003) ‘Physical Network Models and Multi-source Data Integration’.

BibTeX

@article{and2003physical,
  title = {{Physical Network Models and Multi-source Data Integration}},
  author = {And, Chen-Hsiang Yeang and Yeang, Chen-hsiang and Jaakkola, Tommi},
  year = {2003}
}

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