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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...
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...

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Related Experiment Video

Updated: Jun 1, 2026

A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes

Published on: May 22, 2018

Identifier mapping performance for integrating transcriptomics and proteomics experimental results.

Roger S Day1, Kevin K McDade, Uma R Chandran

  • 1Department of Biomedical Informatics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA. day01@pitt.edu

BMC Bioinformatics
|May 31, 2011
PubMed
Summary
This summary is machine-generated.

Comparing proteomic and transcriptomic data requires accurate identifier mapping. Three online tools showed significant discrepancies, highlighting the need for careful selection in omics data integration.

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Area of Science:

  • Biochemistry and Molecular Biology
  • Bioinformatics
  • Genomics and Proteomics

Background:

  • Integrating transcriptomic and proteomic data offers deeper insights into gene-regulatory relationships.
  • Standardization of identifier nomenclature is a significant challenge in multi-omics data integration.
  • Accurate mapping of identifiers is crucial for reliable analysis of high-throughput biological data.

Purpose of the Study:

  • To compare the performance of three freely available online tools for mapping UniProt accessions to Affymetrix probe set IDs.
  • To evaluate the reliability of identifier mapping resources using proteomic and transcriptomic correlation analysis.
  • To provide guidance for selecting appropriate identifier mapping strategies in omics data merging.

Main Methods:

  • Comparison of DAVID, EnVision, and NetAffx for mapping UniProt accessions to Affymetrix probe set IDs.
  • Liquid chromatography-tandem mass spectrometry was used to generate 11,879 distinct UniProt accessions from cancer and non-cancer samples.
  • Proteome-transcriptome correlation analysis was performed to assess the quality of identifier mapping.

Main Results:

  • Significant discrepancies were observed among the three identifier mapping resources.
  • Proteome-transcriptome correlation analysis revealed varying performance levels for the mapping tools.
  • The overall performance of the mapping resources remained consistent over a two-year period despite updates.

Conclusions:

  • The presented methods aid in selecting optimal identifier mapping strategies for omics data integration.
  • Context-specific insights can be gained by critically evaluating different mapping resources.
  • Informed decisions regarding data merging are facilitated by understanding the performance of identifier mapping tools.