# HemaCisDB: An Interactive Database for Analyzing Cis-regulatory Elements Across Hematopoietic Malignancies

## TL;DR

HemaCisDB is a new database that helps researchers study gene regulation in blood cancers by analyzing non-coding DNA regions.

## Contribution

HemaCisDB is a novel interactive platform providing centralized, quality-controlled data and tools for analyzing cis-regulatory elements in hematopoietic malignancies.

## Key findings

- HemaCisDB integrates 922 ATAC-seq, 190 DNase-seq, and 531 H3K27ac ChIP-seq datasets from hematopoietic malignancies.
- The database includes tools for TF footprinting, super-enhancer identification, and regulatory circuitry analysis.
- HemaCisDB enables comparative analysis of TF binding dynamics across different disease types.

## Abstract

Non-coding cis-regulatory elements (CREs), such as transcriptional enhancers, are key regulators of gene expression programs. Accessible chromatin and H3K27ac are well-recognized markers for CREs associated with their biological function. Deregulation of CREs is commonly found in hematopoietic malignancies, yet the extent to which CRE dysfunction contributes to pathophysiology remains incompletely understood. Here, we developed HemaCisDB, an interactive, comprehensive, and centralized online resource for CRE characterization across hematopoietic malignancies, serving as a useful resource for investigating the pathological roles of CREs in blood disorders. Currently, we collected 922 assay of transposase accessible chromatin with sequencing (ATAC-seq), 190 DNase I hypersensitive site sequencing (DNase-seq), and 531 H3K27ac chromatin immunoprecipitation followed by sequencing (ChIP-seq) datasets from patient samples and cell lines across different myeloid and lymphoid neoplasms. HemaCisDB provides comprehensive quality control metrics to assess ATAC-seq, DNase-seq, and H3K27ac ChIP-seq data quality. The analytic modules in HemaCisDB include transcription factor (TF) footprinting inference, super-enhancer identification, and core transcriptional regulatory circuitry analysis. Moreover, HemaCisDB also enables the study of TF binding dynamics by comparing TF footprints across different disease types or conditions via web-based interactive analysis. Together, HemaCisDB provides an interactive platform for CRE characterization to facilitate mechanistic studies of transcriptional regulation in hematopoietic malignancies. HemaCisDB is available at https://hemacisdb.chinablood.com.cn/.

Graphical Abstract