Pathway recognition algorithm using data integration on genomic models (paradigm)

Abstract

A patient sample specific dynamic pathway map is constructed on the basis of measured patient data and a probabilistic pathway model that is based on attributes for pathway elements, wherein some attributes for pathway elements are known a priori, where other attributes for the pathway elements are assumed, and where the pathway elements are cross-correlated and assigned an influence level for at least one pathway. Preferred dynamic pathway maps provide context of the measured patient data with respect to a selected reference pathway activity.

What is claimed is: 
     
         1 . A method of analyzing biologically relevant information, comprising:
 providing access to a pathway database storing a plurality of pathways, wherein at least one of the pathways has an a priori known association with a neoplastic disease;
 wherein each of the plurality of pathways comprises a plurality of respective a priori known pathway elements, and wherein at least some of the a priori known pathway elements have an assumed or previously determined attribute; 
   providing access to a modification engine coupled to the pathway element database;   associating, via the modification engine, at least some of the pathway elements with at least one measured attribute, respectively, wherein the measured attribute is obtained from a patient sample;   determining, via the modification engine, statistically a deregulation score for the at least some of the pathway elements based on the respective measured attributes and assumed or previously determined attributes; and   updating, via the modification engine, a patient sample record using the deregulation score for the at least some of the pathway elements.   
     
     
         2 . The method of  claim 1  wherein the pathway is within a regulatory pathway network. 
     
     
         3 . The method of  claim 2  wherein the regulatory pathway network is selected from the group consisting of an ageing pathway network, an apoptosis pathway network, a homeostasis pathway network, a metabolic pathway network, a replication pathway network, and an immune response pathway network. 
     
     
         4 . The method of  claim 1  wherein the neoplastic disease is a cancer of at least one of the following: a liver, a breast, a lung, a prostate, a cervix, a colon, a pancreas, a brain and skin. 
     
     
         5 . The method of  claim 1  wherein the neoplastic disease is a hyperplasia of the prostate or the thyroid. 
     
     
         6 . The method of  claim 1  wherein the assumed or previously determined attribute of at least some of the a priori known pathway elements is reflective of normal tissue. 
     
     
         7 . The method of  claim 1  wherein the assumed or previously determined attribute of at least some of the a priori known pathway elements is reflective of diseased tissue. 
     
     
         8 . The method of  claim 1  wherein the assumed or previously determined attribute is selected from the group consisting of a compound attribute, a class attribute, a gene copy number, a transcription level, a translation level, and a protein activity. 
     
     
         9 . The method of  claim 8  wherein the assumed or previously determined attribute is a transcription level. 
     
     
         10 . The method of  claim 8  wherein the assumed or previously determined attribute is a translation level or protein activity. 
     
     
         11 . The method of  claim 1  wherein the measured attribute is selected from the group consisting of a compound attribute, a class attribute, a gene copy number, a transcription level, a translation level, and a protein activity. 
     
     
         12 . The method of  claim 11  wherein the measured attribute is a transcription level. 
     
     
         13 . The method of  claim 11  wherein the measured attribute is a translation level or protein activity. 
     
     
         14 . The method of  claim 11  wherein the patient sample comprises a diseased tissue. 
     
     
         15 . The method of  claim 11  wherein the diseased tissue comprises a neoplastic tissue. 
     
     
         16 . The method of  claim 1  wherein statistical determination comprises cross-correlation of the measured attributes and assumed or previously determined attributes for the respective the pathway elements. 
     
     
         17 . The method of  claim 16 , wherein the cross-correlation includes executing an implementation of at least one of the following on the measured attributes and assumed or previously determined attributes for the respective the pathway elements: multi-variant analysis, genetic algorithm, and inference reasoning. 
     
     
         18 . The method of  claim 1  wherein the statistical determination comprises executing statistical simulations.