HSAGEing: an improved SAGE-based software for identification of human tissue-specific or common tumor markers and suppressors.

ABSTRACT:

Background

SAGE (serial analysis of gene expression) is a powerful method of analyzing gene expression for the entire transcriptome. There are currently many well-developed SAGE tools. However, the cross-comparison of different tissues is seldom addressed, thus limiting the identification of common- and tissue-specific tumor markers.

Methodology/principal findings

To improve the SAGE mining methods, we propose a novel function for cross-tissue comparison of SAGE data by combining the mathematical set theory and logic with a unique "multi-pool method" that analyzes multiple pools of pair-wise case controls individually. When all the settings are in "inclusion", the common SAGE tag sequences are mined. When one tissue type is in "inclusion" and the other types of tissues are n

SUBMITTER: Yang CH 

PROVIDER: S-EPMC3003683 | biostudies-literature | 2010 Dec

REPOSITORIES: biostudies-literature