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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form dimers that...
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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Related Experiment Video

Updated: Jun 18, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Published on: February 7, 2019

Transcription factor binding site detection through position cross-mutual information variability analysis.

Joan Maynou1, Montserrat Vallverdu, Francesc Claria

  • 1Dep. ESAII, Centre for Biomedical Engineering Research, Technical University of Catalonia (UPC), Barcelona, Gargallo, 5, 08028 Barcelona, Spain. joan.maynou@upc.edu

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference
|December 8, 2009
PubMed
Summary

This study introduces a novel computational method for detecting transcription factor binding sites by analyzing sequence position correlations. The approach improves the accuracy of identifying these crucial regulatory elements in DNA.

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Related Experiment Videos

Last Updated: Jun 18, 2026

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
06:38

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

Published on: February 7, 2019

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
12:24

PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

Published on: July 2, 2010

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

Area of Science:

  • Computational biology
  • Bioinformatics
  • Genomics

Background:

  • Transcription factor binding site (TFBS) detection is vital for understanding gene regulation.
  • Variability in TFBS sequences complicates computational identification.
  • Accurate TFBS identification is essential for deciphering gene expression patterns.

Purpose of the Study:

  • To propose a novel computational method for detecting transcription factor binding sites.
  • To address the challenge of sequence variability in binding site detection.
  • To evaluate the proposed method's efficiency compared to existing tools.

Main Methods:

  • Utilized information-theoretic measures to capture correlations between binding sequence positions.
  • Developed a novel algorithm for regulatory sequence detection.
  • Employed Receiver Operating Characteristic (ROC) curves to assess detection efficiency.
  • Tested the method on transcription factors in Saccharomyces cerevisiae.

Main Results:

  • The proposed method demonstrates effective detection of transcription factor binding sites.
  • Performance was evaluated using ROC curves, showing competitive efficiency.
  • Results were compared against the Motif Discovery scan (MDscan) algorithm.
  • The method successfully identified binding sites despite sequence variability.

Conclusions:

  • The developed method offers a robust approach for TFBS detection.
  • Information-theoretic measures provide valuable insights into binding site characteristics.
  • This technique enhances computational biology tools for regulatory sequence analysis.
  • The findings contribute to a better understanding of gene regulation mechanisms.