Please use this identifier to cite or link to this item:http://hdl.handle.net/20.500.12105/7672
The multi-reference contrast method: facilitating set enrichment analysis
Comput Biol Med. 2012; 42(2):188-94
Set enrichment analysis (SEA) is used to identify enriched biological categories/terms within high-throughput differential expression experiments. This is done by evaluating the proportion of differentially expressed genes against a background reference (BR). However, the choice of the "appropriate" BR is a perplexing problem and results will depend on it. Here, a visualization procedure that integrates results from several BRs and a stability analysis of enriched terms is presented as a tool to aid SEA. The multi-reference contrast method (MRCM) combines results from multiple BRs in a unique picture. The application of the proposed method was illustrated in one proteomic and three microarray experiments. The MRCM facilitates the exploration task involved in ontology analysis on proteomic/genomic experiments, where consensus terms were found to validate main experimental hypothesis. The use of more than one reference may provide new biological insights. The tool automatically highlights non-consensus terms assisting SEA.
Animals | Cluster Analysis | Data Mining | Electrophoresis, Gel, Two-Dimensional | Gene Expression Profiling | Genomics | Humans | Mice | Models, Theoretical | Oligonucleotide Array Sequence Analysis | Proteomics | Databases, Genetic | Terminology as Topic
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