SYSTEMS AND METHODS FOR NETWORK-BASED BIOLOGICAL ACTIVITY ASSESSMENT
First Claim
1. A computerized method for quantifying perturbation of a biological system, comprisingreceiving, at a first processor, a first set of treatment data corresponding to a response of a first set of biological entities to a first treatment, wherein a first biological system comprises biological entities including the first set of biological entities and a second set of biological entities, each biological entity in the first biological system interacting with at least one other of the biological entities in the first biological system;
- receiving, at a second processor, a second set of treatment data corresponding to a response of the first set of biological entities to a second treatment different from the first treatment;
providing, at a third processor, a first computational causal network model that represents the first biological system and includes;
a first set of nodes representing the first set of biological entities,a second set of nodes representing the second set of biological entities,edges connecting nodes and representing relationships between the biological entities, anddirection values, representing an expected direction of change between the first treatment data and the second treatment data;
calculating, with a fourth processor, a first set of activity measures representing a difference between the first treatment data and the second treatment data for corresponding nodes in the first set of nodes;
generating, with a fifth processor, a second set of activity values for corresponding nodes in the second set of nodes, based on the first computational causal network model and the first set of activity measures.
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Abstract
Systems and methods are disclosed herein for quantifying the response of a biological system to one or more perturbations based on measured activity data from a subset of the entities in the biological system. Based on the activity data and a network model of the biological system that describes the relationships between measured and non-measured entities, activities of entities that are not measured are inferred. The inferred activities are used for deriving a score quantifying the response of the biological system to a perturbation such as a response to a treatment condition. The score may be representative of the magnitude and topological distribution of the response of the network to the perturbation.
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Citations
17 Claims
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1. A computerized method for quantifying perturbation of a biological system, comprising
receiving, at a first processor, a first set of treatment data corresponding to a response of a first set of biological entities to a first treatment, wherein a first biological system comprises biological entities including the first set of biological entities and a second set of biological entities, each biological entity in the first biological system interacting with at least one other of the biological entities in the first biological system; -
receiving, at a second processor, a second set of treatment data corresponding to a response of the first set of biological entities to a second treatment different from the first treatment; providing, at a third processor, a first computational causal network model that represents the first biological system and includes; a first set of nodes representing the first set of biological entities, a second set of nodes representing the second set of biological entities, edges connecting nodes and representing relationships between the biological entities, and direction values, representing an expected direction of change between the first treatment data and the second treatment data; calculating, with a fourth processor, a first set of activity measures representing a difference between the first treatment data and the second treatment data for corresponding nodes in the first set of nodes; generating, with a fifth processor, a second set of activity values for corresponding nodes in the second set of nodes, based on the first computational causal network model and the first set of activity measures. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17)
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Specification