An ensemble method for querying gene expression compendia with experimental lists.

Query-based biclustering can be used to explore public gene expression data for genes coexpressed with genes of interest to a certain researcher (the query). These methods, however, fail when faced with a list of query-genes with diverse expression profiles. In addition, a threshold on the minimal coexpression with the query-genes needs to be defined in advance. To deal with these problems we introduce an ensemble approach for query-based biclustering. The method relies on a specifically designed consensus matrix in which the biclustering outcomes for multiple query-genes and for different possible coexpression thresholds are merged in a statistically robust way. Graph clustering is used to obtain non-redundant consensus biclusters from this matrix. We tested out different ensemble construction schemes and illustrate the effectiveness of this approach.

De Smet, R., Marchal, K. (2010) An ensemble method for querying gene expression compendia with experimental lists. Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM2010) 314-318, Hong Kong, China.

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