Method for determining biological expression levels by linear programming

Ridgway Scott, L., Wright, Stephen, Kurtz, Stuart, Clark, Terry, Dyanov, Chris and Quigg, Richard (2006). Method for determining biological expression levels by linear programming. 7031845.


Creator Ridgway Scott, L.
Wright, Stephen
Kurtz, Stuart
Clark, Terry
Dyanov, Chris
Quigg, Richard
Patent title Method for determining biological expression levels by linear programming
Date of issue 2006-04-18
Year available 2006
Patent owner University of Chicago
Patent number 7031845
Country of origin Chicago, IL
Language eng
Subjects 0604 Genetics
Abstract/Summary A method for determining a matrix of expression levels corresponding to a set of biological targets (e.g., genes or gene fragments) and a set of biological samples, including obtaining a matrix of signal values corresponding to the set of biological targets; computing a vector of expression levels for a sample in the set of biological samples using the matrix of signal values; storing the vector of computed expression levels in a storage matrix; repeating the computing and storing steps for each sample in the set of biological samples; and outputting the storage matrix as the matrix of expression levels. The method, based on a linear programming formulation of the problem, works for both "promiscuous" probe array data, in which there may be multiple targets indicated by a single probe, and the "polygamous" case, in which there are multiple probes for a single target. The preferred method can also process data obtained from multiple SAGE analyses using multiple markers. A second embodiment of the method determines optimal expression levels when the available probe data is noisy or uncertain.
Additional Notes Application number: 10/198,141 Publication number: US 2004/0014044 A1

Document type: Patent
Collection: School of Agriculture and Food Sciences
 
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Created: Thu, 15 Jul 2010, 13:27:48 EST by Thelma Whitbourne on behalf of Faculty Of Nat Resources, Agric & Veterinary Sc