# iSCREEN: An Integrative Data and Annotation Platform of Gene Regulation for Immune-mediated Disease Research

> **NIH NIH U01** · UNIV OF MASSACHUSETTS MED SCH WORCESTER · 2024 · $502,202

## Abstract

In recent years, developments in deep-sequencing-based genomic assays, single-cell technologies, and
machine learning methods have greatly improved our understanding of epigenetics and gene regulation, which
in turn has advanced our understanding of cell type differentiation and human disease. Recent studies have
begun to apply these techniques to understand how non-coding regulatory elements, such as enhancers and
insulators, contribute to infectious, autoinflammatory, and autoimmune diseases. Studies of the immune
system, especially hematopoiesis and genome-wide associations of autoimmune diseases and blood-cell
traits, have produced promising results, discovering unique enhancer landscapes of immune cell types and
identifying genetic variants with clinical relevance for prognosis and treatment of immune diseases. However,
many existing analyses are gene-centric and do not take advantage of regulatory information in non-coding
regions, leaving these data underutilized. An atlas of regulatory elements and their impact on molecular and
clinical phenotypes will greatly expand our understanding of the biology of immune-related diseases and has
the potential to expand precision medicine for predicting clinical outcomes and treatment pathways.
As members of the ENCODE project, we have developed the Registry of candidate cis-regulatory elements
(cCREs), a collection of roughly two million candidate enhancers, promoters, and insulators in the human
genome with activity profiles in more than 1500 human cell types, presented by a powerful web-based
knowledgebase SCREEN (screen.encodeproject.org). The Registry and SCREEN are powerful resources for
the study of non-coding elements, but they do not include any disease-specific data and are not designed to
take advantage of special features of immune data or immune-related disorders. Here, we propose to draw on
the wealth of genomic and epigenetic data from immune samples rapidly accumulating in the literature and
public repositories to build a data integration and visualization platform, iSCREEN, for supporting a wide range
of immune-mediated disease research. This project has three aims: Aim 1. Develop a web-based data
integration platform iSCREEN for immune cCREs and their cell-type-specific epigenetic signals with the goal of
predicting the impact of human genetic variants on immune traits; Aim 2. Build analysis and visualization tools
to map single-cell data onto the space of well-annotated immune cell types and integrate their annotations; and
Aim 3. Perform community outreach, expand our user base, and develop new computational tools and
visualizations to meet user needs.

## Key facts

- **NIH application ID:** 10873829
- **Project number:** 5U01AI173584-03
- **Recipient organization:** UNIV OF MASSACHUSETTS MED SCH WORCESTER
- **Principal Investigator:** Zhiping Weng
- **Activity code:** U01 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $502,202
- **Award type:** 5
- **Project period:** 2022-09-12 → 2026-06-30

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10873829

## Citation

> US National Institutes of Health, RePORTER application 10873829, iSCREEN: An Integrative Data and Annotation Platform of Gene Regulation for Immune-mediated Disease Research (5U01AI173584-03). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10873829. Licensed CC0.

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