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Related Concept Videos

Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
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...
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...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...

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Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics
08:09

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Published on: June 17, 2012

Modular gene expression in Poplar: a multilayer network approach.

Andreas Grönlund1, Rishikesh P Bhalerao1, Jan Karlsson1

  • 1Umeå Plant Science Center Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83 Umeå, Sweden;Umeå Plant Science Center, Department of Plant Physiology, Umeå University, SE-901 87 Umeå, Sweden;Computational Life Science Cluster (CLIC), KBC, Umeå University, SE-901 87 Umeå, Sweden.

The New Phytologist
|January 6, 2009
PubMed
Summary
This summary is machine-generated.

This study introduces a multilayer network approach to analyze Poplar gene expression data, revealing a genome-wide coexpression network. The findings highlight a modular architecture and tissue-specific gene activity patterns.

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Area of Science:

  • Systems Biology
  • Bioinformatics
  • Plant Genomics

Background:

  • Understanding genome-wide gene coexpression is crucial for deciphering complex biological processes in plants.
  • Previous network approaches have limitations in capturing the dynamic and context-specific nature of gene interactions.

Purpose of the Study:

  • To develop and apply a multilayer network approach for exploring genome-wide coexpression in Poplar.
  • To investigate the topological properties and modular architecture of the Poplar coexpression network.
  • To correlate network modules with tissue-specific gene activity patterns.

Main Methods:

  • Construction of multilayer networks using minimum spanning trees (MSTs) generated via Kruskal's algorithm on jack-knifed Poplar microarray data.
  • Generation of a final genome-wide coexpression network by uniting MSTs from random resamplings.
  • Analysis of network topology, modularity, and gene expression patterns across different tissues.

Main Results:

  • The Poplar coexpression network exhibits a highly clustered topology, with increased clustering observed when incorporating links present in fewer MSTs.
  • A modular architecture was identified, indicating functional gene groups with high intra-module communication.
  • The modular structure shows significant overlap with distinct gene activities across different tissues, with related tissues displaying similar expression patterns at the module level.

Conclusions:

  • The multilayer network approach effectively reveals the genome-wide coexpression landscape in Poplar.
  • Rarely appearing links in MSTs can represent significant biological signals rather than noise, enhancing network information quality.
  • The identified modular structure and its tissue-specific activity provide insights into Poplar's functional organization and adaptation.