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Related Concept Videos

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 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 Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
Protein Complexes with Interchangeable Parts01:57

Protein Complexes with Interchangeable Parts

Groups of proteins may form a complex where each protein in this complex has a different role in the overall execution of the complex’s function. Often some of the proteins in the complex can be replaced by a closely related variant to give a complex that contains many of the same components yet is functionally distinct.
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order to...
piRNA - Piwi-interacting RNAs02:57

piRNA - Piwi-interacting RNAs

PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...

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Mapping Dysfunctional Protein-Protein Interactions in Disease
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ppiTrim: constructing non-redundant and up-to-date interactomes.

Aleksandar Stojmirović1, Yi-Kuo Yu

  • 1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.

Database : the Journal of Biological Databases and Curation
|August 30, 2011
PubMed
Summary

A new script, ppiTrim, creates accurate protein interaction datasets by removing redundancy and standardizing annotations. It processes the iRefIndex database to provide reliable data for interactome analysis.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Systems Biology

Background:

  • Robust interactome analysis requires comprehensive, non-redundant, and consistently annotated data.
  • Existing databases like iRefIndex offer improved comprehensiveness but retain original annotations and complex representations, necessitating further user processing.
  • Discrepancies in annotation and representation of protein complexes across databases hinder reliable data consolidation.

Purpose of the Study:

  • To develop a computational tool, ppiTrim, for processing the iRefIndex database.
  • To generate non-redundant and consistently annotated datasets of physical protein-protein interactions.
  • To address challenges in data consolidation, including redundant evidence and varied protein complex representations.

Main Methods:

  • Developed ppiTrim, a script processing iRefIndex in three stages: gene identifier mapping and raw interaction filtering, deflation of expanded protein complexes, and reconciliation of annotation labels.
  • Applied ppiTrim to large-scale interactome datasets for yeast, human, and fruitfly.
  • Evaluated the script's ability to resolve annotation conflicts and standardize interaction data.

Main Results:

  • ppiTrim successfully produces non-redundant and consistently annotated datasets of physical interactions.
  • The script effectively deflates expanded protein complexes into flat lists of members.
  • While most annotation conflicts were resolved, some unresolvable disagreements persisted, primarily due to differing repository annotation policies.

Conclusions:

  • ppiTrim provides a robust solution for generating high-quality, reliable protein-protein interaction data.
  • The script enhances the usability of large interactome databases by standardizing annotations and interaction representations.
  • Further development may be needed to address persistent annotation discrepancies arising from diverse data curation practices.