A new algorithm for comparing and visualizing relationships between hierarchical and flat gene expression data clusterings.
BACKGROUND
Clustering is one of the most widely used methods in unsupervised gene expression data analysis. The use of different clustering algorithms or different parameters often produces rather different results on the same data. Biological interpretation of multiple clustering results requires understanding how different clusters relate to each other. It is particularly non-trivial to compare the results of a hierarchical and a flat, e.g. k-means, clustering.


RESULTS
We present a new method for comparing and visualizing relationships between different clustering results, either flat versus flat, or flat versus hierarchical. When comparing a flat clustering to a hierarchical clustering, the algorithm cuts different branches in the hierarchical tree at different levels to optimize the correspondence between the clusters. The optimization function is based on graph layout aesthetics or on mutual information. The clusters are displayed using a bipartite graph where the edges are weighted proportionally to the number of common elements in the respective clusters and the weighted number of crossings is minimized. The performance of the algorithm is tested using simulated and real gene expression data. The algorithm is implemented in the online gene expression data analysis tool Expression Profiler.


BACKGROUND
http://www.ebi.ac.uk/expressionprofiler
Torrente
Aurora
A
EMBL Outstation-Hinxton, European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. aurora@ebi.ac.uk
Kapushesky
Misha
M
Brazma
Alvis
A
D000465:Algorithms; D016000:Cluster Analysis; D003196:Computer Graphics; D020869:Gene Expression Profiling / Q000379:methods*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010363:Pattern Recognition, Automated / Q000379:methods*; D014584:User-Computer Interface