Identification of the modes of action of bioactive compounds is an important issue in chemical systems biology. In this chapter we review a recently developed data-driven approach using large-scale chemically induced transcriptome data acquired from the Library of Integrated Network-based Cellular Signatures to elucidate the modes of action of bioactive compounds. First, we present a method for pathway enrichment analyses of regulated genes to reveal biological pathways activated by compounds. Next, we present a method using the pre-knowledge on chemical–protein interactome for predicting potential target proteins, including primary targets and off-targets, with transcriptional similarity. Finally, we present a method based on the target proteins for predicting new therapeutic indications for a variety of diseases. These approaches are expected to be useful for mode-of-action analysis, drug discovery, and drug repositioning.
CITATION STYLE
Iwata, M., & Yamanishi, Y. (2019). The use of large-scale chemically-induced transcriptome data acquired from lincs to study small molecules. In Methods in Molecular Biology (Vol. 1888, pp. 189–203). Humana Press Inc. https://doi.org/10.1007/978-1-4939-8891-4_11
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