Understanding the Regulatory Features of Co-regulated Genes Using Distant Regulatory Elements (DiRE) Genomic Tool in Health and Disease

  • Arif MohammedEmail author
  • Othman A. Alghamdi
  • Mohd Rehan
  • Babajan Banaganapalli
  • Ramu Elango
  • Noor Ahmad ShaikEmail author


Regulation of gene expression is a complex process which require several players working together in different time and space in a cell or tissue level. In eukaryotes, gene expression regulation is maintained by a complicated dynamic interplay between proximal promoters and distal regulatory elements (REs) such as repressors and enhancers and transcription factors (TFs). TFs are an important regulator of various life processes and diseases. Ample evidence now suggests that the regulatory networks and the interactions between target binding sites and various TFs play pivotal role in several diseases including cancers. TFs also play a key role in differential gene expression which has proven important in understanding the biological differences between healthy and diseased states. In this book chapter, we discuss about a genomic tool named DiRE which can predict distant REs based on transcription factor binding sites (TFBSs). It possesses a unique capacity to detect REs beyond regions of proximal promoter. DiRE can predict common REs in the coregulated genes. Here we describe step by step method to use this tool. At last, we also discuss the advantages and possible limitation of this tool use for genomic applications.


Gene expression Transcription Transcription factors Genome Database Enhancer Disease 



Differentially Expressed Gene


Distant Regulatory Elements


Evolutionary Conserved Region


Enhancer Identification


Genome-Wide Association Studies


Regulatory Elements


Transcription Factor


Transcription Factor Binding Site


Transcriptional Start Site


Untranslated Regions


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Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Arif Mohammed
    • 1
    Email author
  • Othman A. Alghamdi
    • 1
  • Mohd Rehan
    • 2
    • 3
  • Babajan Banaganapalli
    • 4
  • Ramu Elango
    • 4
  • Noor Ahmad Shaik
    • 4
    Email author
  1. 1.Biology Department, Faculty of SciencesUniversity of JeddahJeddahSaudi Arabia
  2. 2.King Fahd Medical Research Center, King Abdulaziz UniversityJeddahSaudi Arabia
  3. 3.Department of Medical Laboratory Technology, Faculty of Applied Medical SciencesKing Abdulaziz UniversityJeddahSaudi Arabia
  4. 4.Princess Al-Jawhara Center of Excellence in Research of Hereditary DisordersDepartment of Genetic Medicine, Faculty of Medicine, King Abdulaziz UniversityJeddahSaudi Arabia

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