Gene Signature-Based Drug Repositioning

Abstract

With the advent of dynamical omics technology, especially the transcriptome and proteome, a huge amount of data related to various diseases and approved drugs are available under multi global projects or researches with their interests. These omics data and new machine learning technology largely promote the translation of drug research into clinical trials. We will cover the following topics in this chapter. 1) An introduction to the basic discipline of gene signature-based drug repurposing; 2) databases of genes, drugs and diseases; 3) gene signature databases of the approved drugs; 4) gene signature databases of various diseases; 5) gene signature-based methods and tools for drug repositioning; 6) new omics technology for drug repositioning; 7) drug repositioning examples with reproducible code. And finally, discuss the future trends and conclude.

Applying a Gene Reversal Rate Computational Methodology to Identify Drugs for a Rare Cancer: Inflammatory Breast Cancer

“…Gene expression reversal methodology is increasingly being utilized to identify potential drugs for repurposing. 1 - 4 The underlying assumption of these approaches is that a disease can be treated by a drug that has been shown to revert the disease related gene expression signature (GES) back to a normal gene expression state. This approach has been enabled by the fast growth of large publically available gene expression databases such as GEO (Gene Expression Omnibus) at the National Center for Biotechnology Information (NCBI), 5 the large-scale perturbation database termed Connectivity Map (CMap), 6 and the Library of Integrated Network-Based Cellular Signatures (LINCS).…”