The Use of Large-Scale Chemically-Induced Transcriptome Data Acquired from LINCS to Study Small Molecules

  • Michio Iwata
  • Yoshihiro YamanishiEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1888)


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.

Key words

Bioactive compound Drug repositioning Drug target Modes of action Transcriptome Pathway activity 



This work is supported by JST PRESTO Grant Number JPMJPR15D8.


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems EngineeringKyushu Institute of TechnologyFukuokaJapan
  2. 2.PRESTOJapan Science and Technology AgencyKawaguchiJapan

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