Your input gene signature is depicted as the rows of the matrix and the expression level of the genes are indicated with red or blue label-bars (indicating up or down expression).

The top ranked L1000 perturbations (e.g. those with most similar or anti-similar signatures) are shown as columns with red label-bars that indicate their score. L1000 perturbation gene signatures are depicted as columns of the matrix with red and blue squares indicating their effect on gene expression.