TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database.

ABSTRACT:

Background

As public microarray repositories are constantly growing, we are facing the challenge of designing strategies to provide productive access to the available data.

Methodology

We used a modified version of the Markov clustering algorithm to systematically extract clusters of co-regulated genes from hundreds of microarray datasets stored in the Gene Expression Omnibus database (n = 1,484). This approach led to the definition of 18,250 transcriptional signatures (TS) that were tested for functional enrichment using the DAVID knowledgebase. Over-representation of functional terms was found in a large proportion of these TS (84%). We developed a JAVA application, TBrowser that comes with an open plug-in architecture and whose interface implements a highly sophisticated

SUBMITTER: Lopez F 

PROVIDER: S-EPMC2602602 | biostudies-literature | 2008

REPOSITORIES: biostudies-literature