Figure 1.

Overview of connectivity mapping as a pattern matching between (a) query and (b) reference using a (c) similarity measure illustrating different types of matches (f, g, and h). (a) The query is a directional gene signature ($DS=\{S^{+},S^{-}\}$) signified by a set of up-regulated genes ($S^{+}$ shown as red circles) and a set of down-regulated genes ($S^{-}$ shown as blue circles). (b) The reference is a transcriptomic profile $\mathit{x}$ shown as a vector of log2 transformed fold-change (L2FC) values for each gene (blue and red colors represent down- and up-regulation, respectively). (c) The similarity measure ($SM$) for scoring the match between $DS$ and $\mathit{x}$. (d) A collection of predefined signatures representing sets of genes (e.g., involved in pathways). (e) A collection of transcriptomic profiles for a set of perturbagens. (f) “Positive connection” between $DS$ and $\mathit{x}$ when $S^{+}$ and $S^{-}$ are correlated with up- and down-regulated genes in $\mathit{x}$. A positive connection is a match found when $SM\left(DS,\mathit{x}\right)>0$. (g) “No connection” between $DS$ and $\mathit{x}$ when $S^{+}$ and $S^{-}$ are uncorrelated with up- and down-regulated genes in $\mathit{x}$ (where $SM\left(DS,\mathit{x}\right)\approx 0)$. (h) “Negative connection” between $DS$ and $\mathit{x}$ when $S^{+}$ and $S^{-}$ are anti-correlated with up- and down-regulated genes in $\mathit{x}$. A negative connection is a match found when $SM\left(DS,\mathit{x}\right)<0$.