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Related Concept Videos

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...
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...
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...

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Related Experiment Video

Updated: Jul 18, 2026

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

Using local gene expression similarities to discover regulatory binding site modules.

Bartek Wilczyński1, Torgeir R Hvidsten, Andriy Kryshtafovych

  • 1lnstitute of Mathematics, Polish Academy of Sciences, Warsaw, Poland. bartek@impan.gov.pl <bartek@impan.gov.pl>

BMC Bioinformatics
|November 18, 2006
PubMed
Summary

This study introduces a novel method to identify gene regulation patterns in yeast by linking transcription factor binding sites to gene expression. The approach enhances the accuracy of predicting co-regulated genes using accessible data.

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Area of Science:

  • Computational Biology
  • Genomics
  • Systems Biology

Background:

  • Gene regulation governs cellular function.
  • Understanding transcription factor binding site (TFBS) modules is crucial for deciphering gene expression.
  • Saccharomyces cerevisiae serves as a model organism for studying fundamental biological processes.

Purpose of the Study:

  • To develop and validate a computational framework for identifying gene regulatory patterns.
  • To correlate transcription factor binding site modules in gene promoters with observed gene expression levels.
  • To provide a method for rule generalization applicable to genes with uncharacterized expression profiles.

Main Methods:

  • Implementation of local expression similarity clustering.
  • Application of an exact IF-THEN rule inference algorithm.
  • Utilizing sequence and gene expression data from Saccharomyces cerevisiae.
  • Rule generalization for genes with unknown expression profiles.

Main Results:

  • The framework was tested on publicly available yeast datasets.
  • Statistical analyses compared inferred rules against known co-regulated gene sets using ChIP-Chip data and Gene Ontology annotations.
  • Results were objectively compared with similar published studies.

Conclusions:

  • Local expression similarity clustering significantly improves the quality of inferred gene regulatory rules.
  • The derived rules demonstrate enhanced Gene Ontology functional enrichment and coherence with ChIP-Chip binding data.
  • The approach offers reliable, experimentally verifiable hypotheses on gene co-regulation, applicable to other microbes.