Embodiments of this invention include application of new inferential
methods to analysis of complex biological information, including gene
networks. In some embodiments, disruptant data and/or drug
induction/inhibition data are obtained simultaneously for a number of
genes in an organism. New methods include modifications of Boolean
inferential methods and application of those methods to determining
relationships between expressed genes in organisms. Additional new
methods include modifications of Bayesian inferential methods and
application of those methods to determining cause and effect
relationships between expressed genes, and in some embodiments, for
determining upstream effectors of regulated genes. Additional
modifications of Bayesian methods include use of heterogeneous variance
and different curve fitting methods, including spline functions, to
improve estimation of graphs of networks of expressed genes. Other
embodiments include the use of bootstrapping methods and determination of
edge effects to more accurately provide network information between
expressed genes. Methods of this invention were validated using
information obtained from prior studies, as well as from newly carried
out studies of gene expression.