Prediction of Drug-Target Interactions for Drug Repositioning Only Based on Genomic Expression Similarity
Figure 2
The rationale of batch effect adjustment.
(A) The expression profile (denoted as variable E) in CMap is mainly determined by drug action (component d) and batch effect (component b). While the cell condition may vary from batch to batch, the drug action is relatively consistent. Thus, if batch X and Y include cell cultures treated by the same drug (e.g. drug B), these two drug B related expression profiles reflect homogenous drug action but heterogeneous cell condition. So their difference (denoted as Δ) reflects the variation between batch X and Y. By adding Δ to expression profiles in batch Y, the batch variation is adjusted and the two batches are merged into one. (B) Among the batches with 30 instances or more, we find 10 of them linking to each other by various bridge drugs. Primarily, we merged these 10 batches into a new one. Then other batches sharing bridge drugs with this new batch are further merged to form an even bigger batch. This bridging procedure is repeated until all batches are adjusted.