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Related Concept Videos

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.
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.
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...
Positive Regulator Molecules02:39

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.

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Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays
14:06

Mapping Bacterial Functional Networks and Pathways in Escherichia Coli using Synthetic Genetic Arrays

Published on: November 12, 2012

Regulatory link mapping between organisms.

Rachita Sharma1, Patricia A Evans, Virendrakumar C Bhavsar

  • 1Faculty of Computer Science, University of New Brunswick, Fredericton, NB, Canada. rachita.sharma@unb.ca

BMC Systems Biology
|June 22, 2011
PubMed
Summary
This summary is machine-generated.

This study presents a novel method for inferring gene regulatory networks in non-model organisms by mapping known networks from model organisms. The approach successfully predicted and validated regulatory links using bioinformatics tools and gene expression data.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Gene regulatory network identification is crucial for understanding gene regulation.
  • Limited data hinders network inference in non-model organisms.

Purpose of the Study:

  • To develop a method for mapping gene regulatory networks from model to non-model organisms.
  • To overcome data limitations in non-model organisms for network inference.

Main Methods:

  • Utilized Basic Local Alignment Search Tool (BLAST) and InterProScan for transcription factor mapping.
  • Employed BLAST, transcription factor binding site motifs, and GALF-P tool for target gene mapping.
  • Applied gene expression data and defined rules to validate predicted regulatory links.

Main Results:

  • Successfully mapped regulatory network data from *S. cerevisiae* to *A. thaliana*.
  • Gene expression data analysis helped identify well-supported predicted regulatory links.
  • The combined mapping approach yielded accurate regulatory link predictions.

Conclusions:

  • The proposed method effectively infers gene regulatory networks in non-model organisms.
  • Over two-thirds of predicted regulatory links were verified using gene expression data, demonstrating high accuracy.