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 Non-negative 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 improve upon existing methods. The comparison also shows that our method creates a more simplified view that aids in discovery of biological themes within the list and discards less informative classes from the results.


CONCLUSIONS
The presented method and associated software are useful for the identification and interpretation of biological functions associated with gene lists and are especially useful for the analysis of large lists.
Pehkonen
Petri
P
Department of Neurobiology, A,I, Virtanen-Institute, University of Kuopio P,O, Box 1627, FIN-70211 Kuopio, Finland. petri.pehkonen@uku.fi
Wong
Garry
G
Törönen
Petri
P
D016000:Cluster Analysis; D003627:Data Interpretation, Statistical; D030541:Databases, Genetic; D005189:False Positive Reactions; D020869:Gene Expression Profiling; D023281:Genomics / Q000379:methods; D006861:Hydrogen Peroxide / Q000378:metabolism; D017964:Itraconazole / Q000494:pharmacology; D020411:Oligonucleotide Array Sequence Analysis; D018384:Oxidative Stress; D012984:Software; D012985:Software Design; D015003:Yeasts / Q000187:drug effects / Q000235:genetics / Q000378:metabolism
D017964:Itraconazole; D006861:Hydrogen Peroxide