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

Xinping Cai1,2, Qianru Zhang1,2, Bolin Liu1,2

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Genomics, Proteomics & Bioinformatics
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Summary

HemaCisDB is a new online resource for studying cis-regulatory elements (CREs) in blood cancers. It aids research into how CREs contribute to hematopoietic malignancies and blood disorders.

Keywords:
Cis-regulatory elementDatabaseEpigenetic markerHematopoietic malignancyTranscriptional regulation

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Area of Science:

  • Genomics
  • Transcriptional Regulation
  • Hematology

Background:

  • Noncoding cis-regulatory elements (CREs), including transcriptional enhancers, are crucial for gene expression.
  • Accessible chromatin and H3K27ac mark functional CREs.
  • CRE dysfunction is implicated in hematopoietic malignancies, but its role is not fully understood.

Purpose of the Study:

  • To develop HemaCisDB, an interactive online resource for CRE characterization in hematopoietic malignancies.
  • To facilitate the investigation of CREs' pathological roles in blood disorders.

Main Methods:

  • Collected 922 ATAC-seq, 190 DNase-seq, and 531 H3K27ac ChIP-seq datasets from patient samples and cell lines.
  • Integrated quality control metrics for assessing sequencing data.
  • Developed analytic modules for transcription factor (TF) footprinting, super-enhancer identification, and regulatory circuitry analysis.

Main Results:

  • HemaCisDB provides a centralized platform for CRE analysis across various myeloid and lymphoid neoplasms.
  • The resource includes quality control metrics and tools for TF footprinting and regulatory network analysis.
  • Enables comparative analysis of TF binding dynamics across different disease states.

Conclusions:

  • HemaCisDB offers an interactive tool for CRE characterization in hematopoietic malignancies.
  • Facilitates mechanistic studies of transcriptional regulation in blood cancers.
  • Serves as a valuable resource for understanding CRE dysfunction in hematologic disorders.