Abstract #302117

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JSM 2003 Abstract #302117
Activity Number: 337
Type: Contributed
Date/Time: Wednesday, August 6, 2003 : 8:30 AM to 10:20 AM
Sponsor: Biopharmaceutical Section
Abstract - #302117
Title: "Span" Directed Acyclic Boolean Networks from Array Data
Author(s): Lei Li*+ and Horng-shing Lu
Companies: University of Southern California and National Chiao Yung University
Address: Computational Biology, Los Angeles, CA, 90089,
Keywords: microarray ; pathway ; genomic ; EM algorithm ; model selection ; Boolean network
Abstract:

The study of biological networks is becoming an important part of post-genome research. We are interested in using array data to identify relationships between biological elements, such as genes, mRNAs, proteins, or a mixture of them. Specifically, we define a mathematical structure, directed acyclic Boolean networks, as a tool of modeling pathways embedded in binary arrays. Then we introduce a Bernoulli error mechanism to this structure. The problem of estimating networks is generally a challenging one. This difficulty is characterized in our model by the fact that the inference structure is not regular in the classical sense. We propose an exploratory procedure called "SPAN" for the purpose of reconstructing pathways from array data. For each pair of elements, "SPAN" defines a likelihood-based score which is computed by an E-M algorithm and model selection. Then we choose significant pairwise relationships by ranking their scores. Existing biological knowledge can be incorporated to set a significance threshold. We compare this model with Bayesian networks and show how to encode general data types. Numerical examples are included to illustrate the idea.

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