Pathway-based personalized analysis of breast cancer expression data.

ABSTRACT:

Introduction

Most analyses of high throughput cancer data represent tumors by "atomistic" single-gene properties. Pathifier, a recently introduced method, characterizes a tumor in terms of "coarse grained" pathway-based variables.

Methods

We applied Pathifier to study a very large dataset of 2000 breast cancer samples and 144 normal tissues. Pathifier uses known gene assignments to pathways and biological processes to calculate for each pathway and tumor a Pathway Deregulation Score (PDS). Individual samples are represented in terms of their PDSs calculated for several hundred pathways, and the samples of the data set are analyzed and stratified on the basis of their profiles over these "coarse grained", biologically meaningful variables.

Results

We identified nine tu

SUBMITTER: Livshits A 

PROVIDER: S-EPMC5528809 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature