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Functional Associations by Response Overlap (FARO), a Functional Genomics Approach Matching Gene Expression Phenotypes

Figure 1

Overview of the FARO method.

A large number of gene expression studies from a microarray data repository are analyzed individually, resulting in a compendium of gene expression responses. Each of these responses corresponds to a list of top ranking, differentially expressed genes. A query response, for example a response measured in a new microarray experiment, may then be compared to the compendium responses (cr) and the response overlap in terms of common, differentially expressed genes determined. The strength of an association is determined by the size of the overlap and the result illustrated in a FARO map (bottom right and Figure 2). In the example, the query response demonstrates significant associations to compendium factors 1, 3, 4, and 5. Moreover, it is possible to test if the direction of a response is predominantly dissimilar (factor 4) or congruent (factor 5). This is indicated in the FARO map by a hammerhead or an arrow, respectively.

Figure 1

doi: https://doi.org/10.1371/journal.pone.0000676.g001