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Related Concept Videos

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...
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,...
The Proteasome01:13

The Proteasome

Eukaryotic cells can degrade proteins through several pathways. One of the most important among these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
In this pathway, the target proteins are first tagged with small proteins called ubiquitin. This involves participation of a series of enzymes including— E1 (ubiquitin-activating enzyme), E2 (ubiquitin-conjugating enzyme), and E3 (ubiquitin...

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Related Experiment Video

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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
07:01

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

Reactome pathway analysis to enrich biological discovery in proteomics data sets.

Robin Haw1, Henning Hermjakob, Peter D'Eustachio

  • 1Ontario Institute for Cancer Research, Department of Informatics and Bio-computing, Toronto, ON, Canada.

Proteomics
|July 14, 2011
PubMed
Summary

Reactome is a manually curated database of biological pathways and reactions. It offers tools for pathway analysis and visualization, enabling data mining and modeling for proteomics research.

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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools
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Area of Science:

  • Life Sciences
  • Bioinformatics
  • Systems Biology

Background:

  • Reactome is an open-source, expert-authored, and manually curated database detailing biological reactions, pathways, and processes.
  • It provides a comprehensive resource for understanding complex biological systems.

Purpose of the Study:

  • To present Reactome as a valuable resource for pathway knowledge and data analysis.
  • To highlight the integrated tools for pathway visualization, interaction data overlay, and omics data analysis.

Main Methods:

  • Utilizes a Systems Biology Graphical Notation-like Pathway Browser for intuitive navigation and visualization.
  • Integrates PSI Common Query Interface web services to overlay pathway data with molecular interaction information.
  • Employs Ensembl Compara for generating pathway inferences across multiple species.

Main Results:

  • Offers a web-based interface for pathway exploration and a suite of data analysis tools.
  • Enables overlaying pathway data with molecular interactions from various databases (IntAct, ChEMBL, BioGRID).
  • Provides pathway inferences for 20 species beyond human, facilitating cross-species comparisons.

Conclusions:

  • Reactome serves as a robust platform for data mining, modeling, and analysis of large-scale proteomics datasets.
  • Its curated pathway knowledge and analytical tools support diverse biological research applications.
  • The database and its associated tools are valuable for both navigation and in-depth analysis of biological pathways.