Methods to Analyze Biological Networks
First Claim
1. A method for identifying and ranking new drug targets for a known drug from an interaction data set which comprisesa) collecting a plurality of information units, each of said units containing biochemical data describing an interaction between two interacting molecules,b) constructing an interaction data set from said collected information units, in which each of said molecules represents a node and said interaction between said interacting molecules represents a link between two nodes,c) storing the interaction data set in an extractable form,d) selecting from the interaction data set a list of nodes shown to be altered in a cell upon treatment with said known drug as an algorithmic starting point,e) applying one or more graph theory based algorithms to the interaction data set using each node in the selected list of nodes as a starting point to identify a new list of nodes, connected to each node in the selected list, through any number of interconnected nodes,f) compiling the number of instances in which each node appears in the new list of nodes, andg) selecting as drug targets those molecules corresponding to nodes with the highest number of instances.
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Abstract
The present invention relates to a family of graph-theory based methods for the analysis of intracellular signaling networks created from biomedical literature using data-mining processes or acquired through high-content experiments. The methods of the present invention can be used to identify functional dynamic modules within biological networks that can be analyzed quantitatively for input/output relationships. In particular, the present invention relates to a computer-aided method for the in-silico analysis of signaling and other cellular interaction pathways to rank drug targets, identify biomarkers, predict side effects, and classify/diagnose patients.
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Citations
27 Claims
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1. A method for identifying and ranking new drug targets for a known drug from an interaction data set which comprises
a) collecting a plurality of information units, each of said units containing biochemical data describing an interaction between two interacting molecules, b) constructing an interaction data set from said collected information units, in which each of said molecules represents a node and said interaction between said interacting molecules represents a link between two nodes, c) storing the interaction data set in an extractable form, d) selecting from the interaction data set a list of nodes shown to be altered in a cell upon treatment with said known drug as an algorithmic starting point, e) applying one or more graph theory based algorithms to the interaction data set using each node in the selected list of nodes as a starting point to identify a new list of nodes, connected to each node in the selected list, through any number of interconnected nodes, f) compiling the number of instances in which each node appears in the new list of nodes, and g) selecting as drug targets those molecules corresponding to nodes with the highest number of instances.
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15. A method for screening to find potential new drug targets for a known drug using an interaction data set which comprises
a) collecting a plurality of information units, each of said units containing biochemical data describing an interaction between two interacting molecules, b) constructing an interaction data set from said collected information units, in which each of said molecules represents a node and said interaction between said interacting molecules represents a link between two nodes, c) storing the interaction data set in an extractable form, d) selecting from the information data set a node known to interact with said known drug as an algorithmic starting point, e) applying one or more graph theory based algorithms to the interaction data set using the selected node as a starting point to identify a list of nodes connected to the selected node, through any number of interconnected nodes, and f) comparing the number of interconnected nodes between the input node and each node from the list of nodes. g) selecting as potential new drug targets those nodes having the lowest number of interconnected nodes.
Specification