Schematic of the methodology. Only two data sets are shown here; our analysis made use of 60 data sets. The schematic outlines the analysis of a hypothetical “Gene X” in two data sets. First (top) in data set 1 we seek genes with expression profiles that are similar to that of Gene X, generating a set of raw “coexpression links.” Only links that are deemed statistically significant in the context of data set 1 are stored. Then, we repeat this analysis in data set 2 (bottom). We then seek coexpression links that are common between the two data sets. This procedure is then repeated for each gene, and in more data sets. It is important to note that the profiles themselves need not be similar between data sets, nor do the profiles need to be “relevant” to any sample groups in the data sets. The data sets can also be from different microarray platforms, tissues, or species (though we present only human comparisons here). See Methods for details.
