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

Selim Kalayci, Myvizhi Esai Selvan, Irene Ramos, Chris Cotsapas, Eva Harris, Eun Young Kim, Ruth R. Montgomery, Gregory Poland, Bali Pulendran, John S. Tsang, Robert J. Klein, Zeynep H. Gümüş*

*Corresponding author for this work

Research output: Contribution to journalArticle

1 Scopus citations

Abstract

Humans vary considerably both in their baseline and activated immune phenotypes. We developed a user-friendly open-access web portal, ImmuneRegulation, that enables users to interactively explore immune regulatory elements that drive cell-type or cohort-specific gene expression levels. ImmuneRegulation currently provides the largest centrally integrated resource on human transcriptome regulation across whole blood and blood cell types, including (i) ∼43,000 genotyped individuals with associated gene expression data from ∼51,000 experiments, yielding genetic variant-gene expression associations on ∼220 million eQTLs; (ii) 14 million transcription factor (TF)-binding region hits extracted from 1945 ChIP-seq studies; and (iii) the latest GWAS catalog with 67,230 published variant-trait associations. Users can interactively explore associations between queried gene(s) and their regulators (cis-eQTLs, trans-eQTLs or TFs) across multiple cohorts and studies. These regulators may explain genotype-dependent gene expression variations and be critical in selecting the ideal cohorts or cell types for follow-up studies or in developing predictive models. Overall, ImmuneRegulation significantly lowers the barriers between complex immune regulation data and researchers who want rapid, intuitive and high-quality access to the effects of regulatory elements on gene expression in multiple studies to empower investigators in translating these rich data into biological insights and clinical applications, and is freely available at https://immuneregulation.mssm.edu.

Original languageEnglish (US)
Pages (from-to)W142-W150
JournalNucleic acids research
Volume47
Issue numberW1
DOIs
StatePublished - Jul 1 2019

ASJC Scopus subject areas

  • Genetics

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    Kalayci, S., Selvan, M. E., Ramos, I., Cotsapas, C., Harris, E., Kim, E. Y., Montgomery, R. R., Poland, G., Pulendran, B., Tsang, J. S., Klein, R. J., & Gümüş, Z. H. (2019). ImmuneRegulation: a web-based tool for identifying human immune regulatory elements. Nucleic acids research, 47(W1), W142-W150. https://doi.org/10.1093/nar/gkz450