Fig. 1

Using DeDaL for visualizing Fanconi pathway in breast cancer. Top row: standard organic layout (left), PCA-based DDL (right), morphing two previous layouts at half-distance (middle). Bottom row from left to right: PCA-based DDL computed only for basal-like tumors (note change in position of BRCA1 gene), PCA applied to network-smoothed profile, DDL computed using elastic map (elmap) algorithm for computing non-linear principal manifold. Red color denotes larger positive values of the t-test computed for the difference between basal-like and non basal-like groups of samples, green color corresponds to negative values of the t-test