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Related Concept Videos

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...
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...
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the addition of a...
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...
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...
RNA Polymerase II Accessory Proteins02:36

RNA Polymerase II Accessory Proteins

Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...

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Related Experiment Video

Updated: May 18, 2026

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
10:44

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline

Published on: December 7, 2021

Reconstructing dynamic gene regulatory networks from sample-based transcriptional data.

Hailong Zhu1, R Shyama Prasad Rao, Tao Zeng

  • 1Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong, China. hlzhu@comp.hkbu.edu.hk

Nucleic Acids Research
|September 25, 2012
PubMed
Summary

We developed a dynamic cascaded method (DCM) to reconstruct gene regulatory networks from sample-based data. DCM improves network inference and captures dynamic patterns in biological processes like hepatocellular carcinoma progression.

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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Static gene network models fail to capture dynamic biological processes.
  • Dynamic models often require unavailable time-course data.
  • Reconstructing dynamic gene regulatory networks is crucial for understanding complex diseases.

Purpose of the Study:

  • To propose a novel dynamic cascaded method (DCM) for reconstructing dynamic gene networks.
  • To overcome limitations of static and time-course data-dependent dynamic approaches.
  • To apply DCM for analyzing hepatocellular carcinoma (HCC) progression.

Main Methods:

  • Developed the dynamic cascaded method (DCM) based on intra-stage steady-rate and continuity assumptions.
  • Reconstructed dynamic gene networks using sample-based transcriptional data.
  • Applied DCM to HCC progression data and performed functional and network enrichment analyses.

Main Results:

  • DCM successfully reconstructs dynamical networks from sample-based data.
  • DCM significantly improves network inference performance compared to static approaches.
  • Derived HCC networks revealed dynamic patterns, modularity, and network rewiring during disease progression.

Conclusions:

  • DCM offers a robust approach for dynamic gene network reconstruction without time-course data.
  • The method accurately characterizes dynamic and continuous gene transcription.
  • DCM provides insights into the dynamic nature of hepatocellular carcinoma progression.