Clustering chemical prediction lists by biological activity archived in PubChem. A.) A representation of the CTD and chemical-gene sets as shown in detail in Figure 2. B.) Prediction of the chemicals associated to each cancer dataset using chemical-gene sets from the CTD. We selected highly significant chemical predictions for each cancer and clustered these chemicals by their "Bioactivity" similarity as defined and computed in PubChem. C.) Within PubChem, each of these chemicals has a vector of standardized BioAssay scores. PubChem had 790 BioAssay scores for 66 of our significant predictions. The PubChem BioActivity similarity tool uses these vectors of scores to computes the biological activity similarity for each pair of chemicals and similarity is represented as a matrix.
Patel and Butte BMC Medical Genomics 2010 3:17 doi:10.1186/1755-8794-3-17