Constructing networks with correlation maximization methods.
Problems of inference in systems biology are ideally reduced to formulations which can efficiently represent the features of interest. In the case of predicting gene regulation and pathway networks, an important feature which describes connected genes and proteins is the relationship between active and inactive forms, i.e. between the "on" and "off" states of the components. While not optimal at the limits of resolution, these logical relationships between discrete states can often yield good approximations of the behavior in larger complex systems, where exact representation of measurement relationships may be intractable. We explore techniques for extracting binary state variables from measurement of gene expression, and go on to describe robust measures for statistical significance and information that can be applied to many such types of data. We show how statistical strength and information are equivalent criteria in limiting cases, and demonstrate the application of these measures to simple systems of gene regulation.
Mellor
Joseph C
JC
Program in Bioinformatics, Boston University. mellor@bu.edu
Wu
Jie
J
Delisi
Charles
C
D000818:Animals; D015870:Gene Expression; D016681:Genome, Fungal; D007700:Kinetics; D008433:Mathematics; D008954:Models, Biological; D008957:Models, Genetic; D016571:Neural Networks, Computer; D010802:Phylogeny; D011336:Probability; D015203:Reproducibility of Results; D012441:Saccharomyces cerevisiae / Q000235:genetics; D049490:Systems Biology / Q000379:methods*