A seriation approach for visualization-driven discovery of co-expression patterns in Serial Analysis of Gene Expression (SAGE) data.

ABSTRACT:

Background

Serial Analysis of Gene Expression (SAGE) is a DNA sequencing-based method for large-scale gene expression profiling that provides an alternative to microarray analysis. Most analyses of SAGE data aimed at identifying co-expressed genes have been accomplished using various versions of clustering approaches that often result in a number of false positives.

Principal findings

Here we explore the use of seriation, a statistical approach for ordering sets of objects based on their similarity, for large-scale expression pattern discovery in SAGE data. For this specific task we implement a seriation heuristic we term 'progressive construction of contigs' that constructs local chains of related elements by sequentially rearranging margins of the correlation matrix. We ap

SUBMITTER: Morozova O 

PROVIDER: S-EPMC2527533 | biostudies-literature | 2008 Sep

REPOSITORIES: biostudies-literature