Theme discovery from gene lists for identification and viewing of multiple functional groups

Background: High throughput methods of the genome era produce vast amounts of data in the form of gene lists. These lists are large and difficult to interpret without advanced computational or bioinformatic tools. Most existing methods analyse a gene list as a single entity although it is comprised of multiple gene groups associated with separate biological functions. Therefore it is imperative to define and visualize gene groups with unique functionality within gene lists. Results: In order to analyse the functional heterogeneity within a gene list, we have developed a method that clusters genes to groups with homogenous functionalities. The method uses Nonnegative Matrix Factorization (NMF) to create several clustering results with varying numbers of clusters. The obtained clustering results are combined into a simple graphical presentation showing the functional groups over-represented in the analyzed gene list. We demonstrate its performance on two data sets and show results that ...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Petri Pehkonen, Garry Wong, Petri Törönen
• Keywords: BMCBI 2005, Gene Groups, Gene Lists, Multiple Gene Groups