Fig. 1: Data inputs, outputs, and their visual depictions when using the Algorithm for Linking Activity Network (ALAN). Applying the Algorithm for Linking Activity Networks (ALAN).
From: ALAN is a computational approach that interprets genomic findings in the context of tumor ecosystems
Workflow depicting the ALAN algorithm which includes input matrix, matrix generation, user-generated depictions of ALAN data matrices and key terms. Theoretical Connectivity of ALAN. Individual genes are depicted as circles with their respective names (A, B, C, and D). The strength of the correlation between two genes is represented by the thickness of the line. In ALAN Profiles, Profile A (blue) and Profile C (grey) depicted for genes A and C, where the strength of the correlation between the expression patterns of genes (A-A, A-B, A-C, A-D, or C-A, C-B, C-C, C-D) across all samples is represented by the thickness of the line. ALAN Profiles are derived from gene expression correlations, represented by solid lines, across all pairs of genes. In ALAN Network, Network A (blue) and Network C (grey) are depicted for genes A and C, where the strength of the correlation between ALAN profiles (A-A, A-B, A-C, A-D, or C-A, C-B, C-C, C-D) across all genes is represented by the thickness of the line. ALAN Networks are derived from ALAN Profile Correlations, represented by dashed lines, across all pairs of ALAN Profiles. In Depiction of Nominated ALAN Ecosystems, multiple ALAN networks are compared in a two-dimensional space where Networks A and C being more similar are closer together on the plot, whereas shaded dots that are not highlighted represent other ALAN networks for all detected genes.
