Performance comparison of Isomap, PCA and PLS Discriminant Analysis AfCS double ligand screen dataset. Panel A shows cumulative residual variance after the application of Isomap and PCA on the AfCS double ligand screen dataset. Panel B shows two dimensional Isomap projection of the AfCS double ligand screen dataset. Clusters were identified using graph-based clustering with 20-nearest neighbours distance matrix and multilevel k-way partitioning scheme for irregular graphs. Cluster 1 is functionally enriched for interferons, cluster 3 – for TLR ligands and cluster 5 for 2MA, PAF and UDP. Functional coherence scores for all clusters are listed in Additional file 1.