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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...
Constitutive and Regulated Gene Expression01:27

Constitutive and Regulated Gene Expression

Gene expression in prokaryotes is governed by constitutive and regulated systems, allowing cells to balance the production of essential proteins with adaptive responses to environmental changes.Constitutive Gene ExpressionConstitutive, or housekeeping, genes are continuously expressed as they encode proteins vital for fundamental cellular processes. These include enzymes for glycolysis, ribosomal components for protein synthesis, and proteins involved in DNA replication. Their constant...
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...
Combinatorial Gene Control02:33

Combinatorial Gene Control

Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...

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Generating the Transcriptional Regulation View of Transcriptomic Features for Prediction Task and Dark Biomarker Detection on Small Datasets
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A Dataset of Benchmark Boolean Models for Gene Regulatory Networks.

Caya L O Hotstegs1, Jose P Llano1,2, Hans A Kestler3,4

  • 1Institute of Medical Systems Biology, Ulm University, Albert-Einstein-Allee 11, 89081, Ulm, Germany.

Scientific Data
|June 6, 2026
PubMed
Summary
This summary is machine-generated.

This study introduces benchmark Boolean network (BN) models for gene regulatory networks (GRNs) across major kingdoms. These standardized models offer an unbiased approach for evaluating computational methods in systems biology.

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Area of Science:

  • Systems Biology
  • Computational Biology
  • Bioinformatics

Background:

  • Gene regulatory networks (GRNs) govern gene expression.
  • Boolean network (BN) modeling simplifies GRN dynamics analysis.
  • Current BN models often lack real-world biological relevance due to ad hoc construction.

Purpose of the Study:

  • To develop standardized benchmark Boolean network models for gene regulatory networks.
  • To provide unbiased models for evaluating computational methods in systems biology.
  • To represent GRNs from animals, bacteria, fungi, and plants.

Main Methods:

  • Construction of benchmark BN models based on empirical GRN properties and motifs.
  • Development of models representing four major biological kingdoms.
  • Systematic approach to ensure unbiased representation of GRN structures and dynamics.

Main Results:

  • Creation of benchmark BN models for animal, bacterial, fungal, and plant GRNs.
  • Models are derived from recurrent properties and motifs observed in real GRNs.
  • Establishment of a standardized framework for computational method evaluation.

Conclusions:

  • The benchmark BN models offer a robust and unbiased basis for validating GRN analysis algorithms.
  • These models facilitate more reliable comparisons of computational tools in systems biology.
  • The study addresses the need for realistic models in the study of gene regulation.