US 2010/0250143 A1 · IDENTIFYING BIOLOGICAL RESPONSE PATHWAYS

Abstract

A method for identifying a mechanism associated with a cellular response includes identifying molecules participating in the cellular response; accessing a database containing information characterizing molecular interactions; determining pathways connecting the identified molecules participating in the cellular response; and solving an optimization problem that includes determining a subset of the molecules and interactions having a minimum aggregate cost. The pathways include, nodes, each representing a molecule, and edges, each connecting a respective pair of nodes and representing an interaction between a respective pair of molecules represented by the respective pair of nodes. Nodes from a subset of nodes represent molecules identified as participating in the cellular response.

Claims16

Dependent claims

A method for updating a computer-readable data storage medium with the aid of a particular microprocessor tied to said computer-readable data storage medium, said data storage medium containing interaction data, said interaction data being representative of interactions within a cell, said method comprising:

receiving a global measurement of activity in a cell;
causing said microprocessor to retrieve, from a database stored on a computer-readable medium, said interaction data, said interaction data including data representative of
a subset of interactions within the cell, each of said interactions being consistent with said global measurement;
causing said microprocessor to determine an aggregate cost for each of said interactions;
causing said microprocessor to determine which of said interactions from said subset of interactions has a minimum aggregate cost;
causing said microprocessor to provide output representative of said minimum cost interaction;
and
causing said output to be stored in said computer-readable data storage medium.

5 more elements

A method for operating a machine for identifying a mechanism associated with a cellular response with the aid of a digital computer, the method comprising:

identifying molecules participating in the cellular response;
causing the computer to access a database containing information characterizing molecular interactions;
causing the computer to determine pathways connecting the identified molecules participating in the cellular response, wherein the pathways include:
a plurality of nodes, each node representing a molecule, and
a plurality of edges, each edge connecting a respective pair of nodes and representing an interaction between a respective pair of molecules represented by the respective pair of nodes,
wherein the plurality of nodes includes a subset of nodes that represent molecules identified as participating in the cellular response;
and
causing said computer to solve an optimization problem that includes determining a subset of the molecules and interactions having a minimum aggregate cost.

5 more elements

Dependencies are inferred from the claim text.

Identifying biological response pathways

Life of this patent

Identifying biological response pathways

Life of this patent

Abstract

Claims16