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Covalently Linked Protein Regulators

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....

Cooperative Binding of Transcription Regulators

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Cis-regulatory Sequences

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...

Cell Signaling Feedback Loops

Cell Signaling Feedback Loops

Positive and negative feedback loops are crucial for regulating biological signaling systems. These feedback loops are processes that connect output signals to their inputs.
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Most signaling systems have negative feedback loops that can perform different functions such as output limiter, and adaptation.
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Positive Regulator Molecules

Positive Regulator Molecules

Mitotic cell division results in daughter cells that exactly resemble the parent cell. However, errors in the DNA replication or distribution of genetic material may lead to genetic mutations that may be passed down to every new cell formed from the resulting abnormal cell. Propagation of such mutant cells is restricted through checkpoint mechanisms present at different stages of the cell cycle. These checkpoints involve regulator molecules that either promote or demote cell cycle events.

Root Loci for Positive-Feedback Systems

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The Hartley oscillator is a positive feedback system that sustains oscillations by feeding the output back to the input in phase, thereby reinforcing the signal. Positive feedback systems can be viewed as negative feedback systems with inverted feedback signals. In these systems, the root locus encompasses all points on the s-plane where the angle of the system transfer function equals 360 degrees.
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Updated: May 10, 2025

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

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

Published on: December 7, 2021

CORN 2.0 - Condition Orientated Regulatory Networks 2.0.

Ricky Wai Tak Leung^1,2, Xinying Zhang¹, Zhuobin Chen¹

¹School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China.

Computational and Structural Biotechnology Journal

|April 24, 2025

Summary

The Condition-Oriented Regulatory Networks (CORN) database now links thousands of conditions to specific gene regulatory sub-networks. This resource aids research in personalized medicine and natural compound pharmacology.

Keywords:

Cell fate Chinese medicine Embryonic stem cells Gene regulatory network Herbal medicine Induced pluripotency Natural compounds Natural products Personalized medicine Tumor heterogeneity

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Last Updated: May 10, 2025

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Published on: October 6, 2019

Area of Science:

Molecular Biology
Systems Biology
Bioinformatics

Background:

Gene regulation allows organisms to adapt via nucleic acid-binding proteins (NBPs) like transcription factors (TFs).
Transcriptional regulatory networks (TRNs) can be analyzed as condition-specific transcriptional regulatory sub-networks (TRSNs) for stability and practicality.
The Condition-Oriented Regulatory Networks (CORN) database provides condition-based TRSNs.

Purpose of the Study:

To present CORN 2.0, an updated and expanded database of condition-specific TRSNs.
To highlight the utility of CORN 2.0 in personalized medicine, induced pluripotency, and natural compound pharmacology.
To offer a comprehensive resource for studying gene regulation under diverse conditions.

Main Methods:

Curated and integrated data on transcriptional regulatory sub-networks (TRSNs) across various conditions.
Associated 7540 specific conditions with 71934 TRSNs in 52 human cell lines, involving 542 transcription factors (TFs).
Included 1550 natural compound-triggered TRSNs in the CORN 2.0 database.

Main Results:

CORN 2.0 significantly expands the coverage of condition-based TRSNs.
The database links thousands of specific conditions, including natural compounds, to relevant TRSNs.
Demonstrated the application of CORN in personalized medicine, pluripotency, and natural product pharmacology.

Conclusions:

CORN 2.0 is a valuable resource for understanding gene regulation under specific conditions.
The database facilitates research into disease mechanisms and therapeutic interventions.
CORN enables exploration of how gene regulatory networks respond to various stimuli, including natural compounds.