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Related Concept Videos

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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...
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...
Transcription Factors02:16

Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
Transcription Factors02:16

Transcription Factors

Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...

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Genome-wide Snapshot of Chromatin Regulators and States in Xenopus Embryos by ChIP-Seq
10:23

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Published on: February 26, 2015

TREP_DB: transcriptional regulatory elements pattern database.

Hyoung-Sam Heo1, S June Oh, Ji Min Kim

  • 1Department of Pharmacy, College of Pharmacy and Molecular Inflammation Research Center for Aging Intervention, Pusan National University, Gumjung-gu, Busan 609-735, Republic of Korea.

Biochemical and Biophysical Research Communications
|March 9, 2010
PubMed
Summary
This summary is machine-generated.

This study introduces a novel non-homology method for predicting gene functions using transcriptional regulatory elements. This approach enhances the accuracy of function assignment for hypothetical proteins and putative genes.

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Last Updated: Jun 15, 2026

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10:23

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Published on: February 26, 2015

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Accurate function prediction for novel genes is crucial in the post-genomic era.
  • Current homology-based methods have limitations, failing for ~30% of genes and lacking experimental validation for most.
  • Gene co-regulation, indicated by correlated expression profiles, suggests shared transcriptional regulatory elements.

Purpose of the Study:

  • To develop a non-homology-based method for predicting functions of putative genes and hypothetical proteins.
  • To identify patterns of common transcriptional regulatory elements associated with specific functional classes.

Main Methods:

  • Established patterns (combinations) of common transcriptional regulatory elements for mouse functional classes, creating the TREP_DB database.
  • Developed a novel function-prediction method based on these identified patterns.

Main Results:

  • Identified specific patterns of transcriptional regulatory elements linked to distinct gene functional classes in mouse.
  • Demonstrated the utility of these patterns for predicting gene functions.

Conclusions:

  • The proposed non-homology method offers a complementary approach to homology-based predictions.
  • This method has the potential to improve the functional annotation of uncharacterized genes and proteins.