Discovery of surface target proteins linking drugs, molecular markers, gene regulation, protein networks, and disease by using a web-based platform targets-search

Bin Yan, Panwen Wang, Junwen Wang, Kenneth R. Boheler

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

Integration and analysis of high content omics data have been critical to the investigation of molecule interactions (e.g., DNA–protein, protein–protein, chemical–protein) in biological systems. Human proteomic strategies that provide enriched information on cell surface proteins can be utilized for repurposing of drug targets and discovery of disease biomarkers. Although several published resources have proved useful to the analysis of these interactions, our newly developed web-based platform Targets-search has the capability of integrating multiple types of omics data to unravel their association with diverse molecule interactions and disease. Here, we describe how to use Targets-search, for the integrated and systemic exploitation of surface proteins to identify potential drug targets, which can further be used to analyze gene regulation, protein networks, and possible biomarkers for diseases and cancers. To illustrate this process, we have taken data from Ewing’s sarcoma to identify surface proteins differentially expressed in Ewing’s sarcoma cells. These surface proteins were then analyzed to determine which ones were known drug targets. The information suggested putative targets for drug repurposing and subsequent analyses illustrated their regulation by the transcription factor EWSR1.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages331-344
Number of pages14
Volume1722
DOIs
StatePublished - Jan 1 2018

Publication series

NameMethods in Molecular Biology
Volume1722
ISSN (Print)1064-3745

    Fingerprint

Keywords

  • Drug target
  • Molecular marker
  • Surface protein
  • Targets-search
  • Web-based platform

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Yan, B., Wang, P., Wang, J., & Boheler, K. R. (2018). Discovery of surface target proteins linking drugs, molecular markers, gene regulation, protein networks, and disease by using a web-based platform targets-search. In Methods in Molecular Biology (Vol. 1722, pp. 331-344). (Methods in Molecular Biology; Vol. 1722). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7553-2_19