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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...
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...
Global Regulatory Systems01:28

Global Regulatory Systems

Global regulatory systems in bacteria enable rapid and coordinated responses to environmental changes by integrating sensory inputs with gene expression, ensuring efficient adaptation to fluctuating conditions. Key global regulatory mechanisms include regulons, two-component systems, sigma factors, and secondary messengers.Regulons and Global RegulatorsA regulon is a collection of genes and operons controlled by a common global regulator. These regulators enable bacteria to prioritize resource...
Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein.

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Related Experiment Video

Updated: Jul 11, 2026

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

Finding regulatory elements and regulatory motifs: a general probabilistic framework.

Erik van Nimwegen1

  • 1Biozentrum, University of Basel, and Swiss Institute of Bioinformatics, Klingelbergstrasse 50/70, Basel, Switzerland. erik.vannimwegan@unibas.ch

BMC Bioinformatics
|October 2, 2007
PubMed
Summary
This summary is machine-generated.

This study unifies regulatory motif finding algorithms, particularly those using position specific weight matrices (WMs), within a Bayesian probabilistic framework. It demonstrates how various motif discovery and module finding methods are integrated aspects of this single theory.

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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay (EMSA) and DNA-affinity Precipitation Assay (DAPA)
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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Genomics

Background:

  • Numerous algorithms for regulatory motif finding have been developed over the last two decades.
  • Many algorithms utilize position specific weight matrices (WMs) to model regulatory factor binding specificities.

Purpose of the Study:

  • To demonstrate that many existing motif-finding algorithms can be unified within a general Bayesian probabilistic framework.
  • To elucidate the integrated nature of diverse motif discovery and regulatory module finding methods.

Main Methods:

  • Bayesian probabilistic modeling
  • Position specific weight matrix (WM) construction and scanning
  • Expectation maximization (EM) and motif sampling algorithms
  • Integration of motif finding with phylogenetic footprinting

Main Results:

  • Many algorithms, especially those using WMs, naturally emerge from a general Bayesian probabilistic framework.
  • Methods for constructing WMs, discovering sites, clustering WMs, and finding regulatory modules are presented.
  • Phylogenetic information can be rigorously integrated into motif and module finding.

Conclusions:

  • Diverse computational methods for regulatory motif and module discovery are not isolated recipes but facets of a single probabilistic theory.
  • A unified Bayesian framework provides a rigorous approach to motif finding, module discovery, and phylogenetic footprinting.