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ImmuneRegulation: a web-based tool for identifying human immune regulatory elements.

Selim Kalayci1,2, Myvizhi Esai Selvan1,2, Irene Ramos3

  • 1Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

Nucleic Acids Research
|May 23, 2019
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Summary
This summary is machine-generated.

ImmuneRegulation is a new web portal offering a large, integrated resource for exploring human immune gene regulation. It helps researchers understand how genetic variations and regulatory elements influence gene expression across diverse cell types and studies.

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Area of Science:

  • Immunology
  • Genomics
  • Bioinformatics

Background:

  • Human immune responses exhibit significant variability at baseline and during activation.
  • Understanding the genetic and regulatory underpinnings of this variability is crucial for biological and clinical insights.

Purpose of the Study:

  • To develop and present ImmuneRegulation, an open-access web portal for exploring human immune gene regulation.
  • To provide a comprehensive, integrated resource for analyzing transcriptome regulation in whole blood and blood cell types.

Main Methods:

  • Integration of genetic variant-gene expression associations (eQTLs) from ∼43,000 individuals and ∼51,000 experiments.
  • Inclusion of transcription factor (TF) binding data from 1945 ChIP-seq studies (14 million hits).
  • Incorporation of the latest GWAS catalog data (67,230 variant-trait associations).

Main Results:

  • ImmuneRegulation provides access to ∼220 million eQTLs, 14 million TF-binding regions, and 67,230 GWAS catalog entries.
  • Users can interactively explore associations between genes and their regulators (eQTLs, TFs) across multiple cohorts.
  • The portal facilitates the identification of regulators explaining genotype-dependent gene expression and aids in cohort selection for studies.

Conclusions:

  • ImmuneRegulation significantly simplifies access to complex immune regulation data for researchers.
  • The portal empowers the translation of rich genetic and transcriptomic data into biological insights and clinical applications.
  • ImmuneRegulation is freely available at https://immuneregulation.mssm.edu, lowering barriers to data exploration.