Appeal No. 2005-2663 Page 4
Application No. 10/140,323
regulates gene 0, which regulates gene 16, which regulates gene 2, so the adjacency
list of gene 14 is 0 and the accessibility list of gene 14 is 0 2 16. “Generating the list in
Figure 1C from 1A or 1B is straightforward. The present invention addresses the more
difficult problem of reconstructing all direct interactions in a network from all indirect
ones, that is, to reconstruct 1A (Adj) from 1C (Acc), and to do that automatically for very
large networks comprising thousands of genes.” Specification, page 11.
Discussion
1. Claim construction
Claims 1-7, 9, 16, 17, 19, and 20 are on appeal. Claims 8, 11-15, and 18 are
also pending but have been withdrawn from consideration. See the Appeal Brief, page
2. Claim 1-4 are representative of the appealed claims and read as follows:
1. A method for determining all direct and indirect genetic interactions
in a graph representation of a genetic network of an organism,
comprising:
obtaining a first accessibility list of said graph representation of said
genetic network from appropriate genetic perturbation data;
applying graph theory mathematics to the first accessibility list and
its graph to determine a condensation of the graph as defined by
the condensation’s accessibility list;
applying graph theory mathematics to the condensation’s
accessibility list to determine an adjacency list characterizing all
direct and indirect genetic interactions in said genetic network.
2. The method of claim 1, wherein said graph theory mathematics are
applied using a recursive algorithm.
3. The method of claim 2, wherein said recursive algorithm
determines the adjacency list of a most parsimonious graph.
4. The method of claim 2, wherein said recursive algorithm
determines a list of the longest path of said graph.
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