The ParTriCluster Algorithm for Gene Expression Analysis

Analyzing gene expression patterns is becoming a highly relevant task in the Bioinformatics area. This analysis makes it possible to determine the behavior patterns of genes under various conditions, a fundamental information for treating diseases, among other applications. A recent advance in this area is the Tricluster algorithm, which is the first algorithm capable of determining 3D clusters (genes x samples x timestamps), that is, groups of genes that behave similarly across samples and timestamps. However, while biological experiments collect an increasing amount of data to be analyzed and correlated, the triclustering problem is NP-Complete, and its parallelization seems to be an essential step towards obtaining feasible solutions. In this work we propose and evaluate the implementation of a parallel version of the Tricluster algorithm using the filter-labeled-stream paradigm supported by the Anthill parallel programming environment. The results show that our parallelization sca...

• Type: Journal
• Year: 2008
• Where: IJPP
• Authors: Renata Braga Araújo, Guilherme Henrique Trielli Ferreira, Gustavo Henrique Orair, Wagner Meira Jr., Renato Antônio Celso Ferreira, Dorgival Olavo Guedes Neto, Mohammed Javeed Zaki
• Keywords: Gene Expression Patterns, IJPP 2006, IJPP 2008, Parallelization, Tricluster Algorithm