Appeal No. 2005-2663 Page 2
Application No. 10/140,323
The data resulting from such an experiment can show how eliminating the expression of
one gene affects, directly or indirectly, the expression of other genes. Such data
cannot, however, show which genes are directly regulated by a particular gene or how
any indirect regulation takes place.
The specification discloses a “method that can determine the direct and indirect
pathways connecting genes in the network and which genes in a network influence the
activity of which other genes directly. . . . The algorithm’s power to resolve regulatory
gene interactions . . . requires different kinds of data than utilized by existing methods.
Specifically, it requires perturbation of many genes in a network. The required large-
scale data is now becoming available in a variety of model organisms.” Page 4.
The disclosed method applies graph theory mathematics to gene expression
data. The general idea can be grasped from the specification’s Figures 1A – 1C and
explanatory text. Figure 1A is reproduced below:
Figure 1A is “a graph representation of a hypothetical genetic network G of 21 genes.”1
1 In their mathematical representation, the genes are referred to as “nodes” and the regulatory effects are
represented by arrows that are referred to as “directed edges.”
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