Related Experiment Video

Updated: Jul 5, 2025

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries
10:10

HOX Loci Focused CRISPR/sgRNA Library Screening Identifying Critical CTCF Boundaries

Published on: March 31, 2019

8.3K

TSCRE: a comprehensive database for tumor-specific cis-regulatory elements

Guanjie Peng1,2,3, Bingyuan Liu1,2,3, Mohan Zheng2

  • 1Clinical Big Data Research Center, Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen 518107, P.R. China.

NAR Cancer
|January 12, 2024
PubMed

Insights

The TSCRE database catalogs dysregulated cis-regulatory elements (CREs) and super cis-regulatory elements (SCREs) in human cancers. This resource aids in identifying novel cancer biomarkers and understanding gene regulation in tumors.

Area of Science:

  • Genomics and Cancer Biology
  • Non-coding DNA and Gene Regulation

Background:

  • Cis-regulatory elements (CREs) and super cis-regulatory elements (SCREs) are crucial non-coding DNA regions controlling gene transcription and development.
  • Altered CRE and SCRE activity is linked to oncogene and tumor suppressor dysregulation, impacting cancer progression.
  • A comprehensive resource for dysregulated CREs and SCREs in human cancers is needed.

Purpose of the Study:

  • To establish TSCRE, an open-access database cataloging tumor-specific and cell type-specific CREs and SCREs in human cancers.
  • To provide a valuable platform for discovering candidate cancer biomarkers and investigating gene regulatory mechanisms.

Main Methods:

  • Re-analysis of publicly available histone modification profiles from 1366 human patient samples across 17 cancer types.
  • Identification and annotation of dysregulated CREs and SCREs using 9 histone marks.
  • Integration of comprehensive annotations including gene associations, expression, mutations, and clinical data.

Main Results:

  • TSCRE contains 1,864,941 dysregulated CREs and 68,253 dysregulated SCREs.
  • Over 95% of identified elements are validated in public resources.
  • The database offers detailed annotations and integrated pathway/transcription factor enrichment analyses.

Conclusions:

  • TSCRE provides a comprehensive and validated resource for exploring dysregulated CREs and SCREs in human cancers.
  • The platform facilitates in-depth functional investigations and the discovery of potential cancer biomarkers and therapeutic targets.

More Related Videos

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

10.4K
Author Spotlight: Unveiling the Role of TMOD3 in Platinum Resistance and Immune Infiltration in Ovarian Cancer09:40

Author Spotlight: Unveiling the Role of TMOD3 in Platinum Resistance and Immune Infiltration in Ovarian Cancer

Published on: August 2, 2024

2.7K

Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

3.0K
Cancer-Critical Genes II: Tumor Suppressor Genes01:05

Cancer-Critical Genes II: Tumor Suppressor Genes

Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
7.4K
Cancer-Critical Genes I: Proto-oncogenes01:33

Cancer-Critical Genes I: Proto-oncogenes

Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
8.9K
Master Transcription Regulators02:23

Master Transcription Regulators

Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
6.9K
Co-activators and Co-repressors02:04

Co-activators and Co-repressors

Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
7.4K
Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
11.5K