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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Protein Interfaces02:04

Protein-Protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Ribosome Profiling02:24

Ribosome Profiling

Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...
Proteomics01:33

Proteomics

A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term proteomics...

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mRNA Interactome Capture from Plant Protoplasts
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Published on: July 28, 2017

Identifying functional modules using expression profiles and confidence-scored protein interactions.

Igor Ulitsky1, Ron Shamir

  • 1Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.

Bioinformatics (Oxford, England)
|March 20, 2009
PubMed
Summary
This summary is machine-generated.

We developed CEZANNE, a novel method integrating gene expression and protein interaction data to identify functional gene modules. CEZANNE improves interpretation of complex biological data and outperforms existing approaches.

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A Protocol for Computer-Based Protein Structure and Function Prediction
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Published on: November 3, 2011

Area of Science:

  • Bioinformatics
  • Systems Biology
  • Computational Biology

Background:

  • Microarray gene expression studies present interpretation challenges due to high dimensionality.
  • Integrating gene expression with protein interaction networks can improve analysis, but data quality is a limitation.

Purpose of the Study:

  • To present CEZANNE (Co-Expression Zone ANalysis using NEtworks), a novel confidence-based method for extracting functionally coherent co-expressed gene sets.
  • To improve the analysis of gene expression data by integrating it with protein interaction networks.

Main Methods:

  • CEZANNE utilizes probabilities for individual interactions and a probabilistic model.
  • A weighting scheme relates subnetwork connectivity likelihood to minimum cut weight.
  • The method was applied to a Saccharomyces cerevisiae DNA damage response dataset.

Main Results:

  • CEZANNE successfully recovered known and identified novel functional modules.
  • Novel protein functions were predicted.
  • CEZANNE demonstrated superior performance compared to previous methods for analyzing expression and interaction data.

Conclusions:

  • CEZANNE offers a robust approach for identifying functionally coherent gene sets from integrated omics data.
  • The method enhances the interpretation of complex biological datasets, such as those in DNA damage response pathways.
  • CEZANNE is available within the MATISSE software package.