The fundamental unit of CMap analysis is the query. A query (q) consists of a set of genes corresponding to any biological state of interest. Each gene in the query carries a sign indicating whether it is up-regulated or down-regulated. Thus each query yields a pair of mutually exclusive gene lists (qup, qdown). The query is compared to each signature in the CMap reference database (Touchstone) using the similarity metric described below to assess connectivity viz. the degree to which the up-regulated query genes (qup) appear toward the top of the rank-ordered signature and the down-regulated query genes (qdown) appear toward the bottom of the signature (positive connectivity) or vice-versa (negative connectivity). The result of a query is a rank ordered list of CMap signatures ordered by their connectivity scores.
