Empirical comparison of structure-based pathway methods.

ABSTRACT: Multiple methods have been proposed to estimate pathway activities from expression profiles, and yet, there is not enough information available about the performance of those methods. This makes selection of a suitable tool for pathway analysis difficult. Although methods based on simple gene lists have remained the most common approach, various methods that also consider pathway structure have emerged. To provide practical insight about the performance of both list-based and structure-based methods, we tested six different approaches to estimate pathway activities in two different case study settings of different characteristics. The first case study setting involved six renal cell cancer data sets, and the differences between expression profiles of case and control samples were relativel

SUBMITTER: Jaakkola MK 

PROVIDER: S-EPMC4793894 | biostudies-literature | 2016 Mar

REPOSITORIES: biostudies-literature