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Related Concept Videos

Proteomics01:33

Proteomics

8.6K
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...
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A Streamlined Approach for Mass Spectrometry-Based Proteomics Using Selected Tissue Regions
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GO Enrichment Analysis for Differential Proteomics Using ProteoRE.

Florence Combes1, Valentin Loux2,3, Yves Vandenbrouck4

  • 1Université Grenoble Alpes, INSERM, CEA, UMR BioSanté U1292, Grenoble, France.

Methods in Molecular Biology (Clifton, N.J.)
|July 8, 2021
PubMed
Summary
This summary is machine-generated.

ProteoRE offers a user-friendly online service for proteomics data analysis, simplifying functional interpretation for researchers. This tool facilitates biological insights from complex protein datasets without extensive bioinformatics expertise.

Keywords:
Computer applicationEnrichment analysisFunctional annotationGalaxyGene annotationGene ontologyProteomicsWeb server

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • The increasing volume of proteomics data necessitates advanced functional analysis tools.
  • Biologists and clinicians require accessible computational solutions for interpreting proteomics findings.
  • Existing bioinformatics tools often have a steep learning curve for non-experts.

Purpose of the Study:

  • To develop ProteoRE (Proteomics Research Environment), a unified online service for proteomics data interpretation.
  • To provide biologists and clinicians with accessible tools for functional and visual analysis of proteomics datasets.
  • To enable collaborative and reproducible analysis of large protein lists.

Main Methods:

  • ProteoRE is built on the Galaxy framework, integrating a suite of complementary computational tools.
  • A step-by-step protocol for functional annotation and Gene Ontology (GO)-based enrichment analysis is provided.
  • The service offers user-friendly interfaces for interaction with analysis tools.

Main Results:

  • ProteoRE provides a unified platform for functional and visual analysis of proteomics data.
  • A specific protocol demonstrates functional annotation and GO enrichment analysis on differentially expressed proteins.
  • All tools, datasets, and results are freely available for reuse.

Conclusions:

  • ProteoRE addresses the bottleneck in proteomics data analysis by offering an accessible, integrated solution.
  • The platform empowers researchers with limited bioinformatics experience to gain biological insights from their data.
  • The collaborative and reproducible nature of ProteoRE enhances the value of proteomics research.