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g2pDB: A Database Mapping Protein Post-Translational Modifications to Genomic Coordinates.

Sarah Keegan1, John P Cortens2, Ronald C Beavis2

  • 1Center for Health Informatics and Bioinformatics, New York University Medical School , 227 East 30 Street, New York, New York 10016, United States.

Journal of Proteome Research
|February 5, 2016
PubMed
Summary
This summary is machine-generated.

Researchers mapped human post-translational modifications to genomic locations, creating the g2pDB database. This tool links protein changes to DNA variants, aiding in understanding genetic impacts on protein function.

Keywords:
REST APIacetylationgenome coordinatephosphorylationpost-translational modificationprotein coordinatesingle nucleotide variantubiquitination

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Area of Science:

  • Biochemistry
  • Genomics
  • Proteomics

Background:

  • Large-scale proteomics enables broad screening for post-translational modifications (PTMs) like phosphorylation, acetylation, and ubiquitination.
  • PTM data localization to specific peptide sites or domains is crucial for functional annotation.
  • Archiving PTM information onto protein sequences is essential for biological interpretation.

Purpose of the Study:

  • To create a comprehensive map of reproducible human post-translational modification sites.
  • To translate these modification sites into genomic codon coordinates.
  • To develop a database (g2pDB) for linking nucleotide variants to perturbed protein modifications.

Main Methods:

  • Utilized a large archive of experimental human PTM observations.
  • Mapped reproducible modification sites onto complete human protein sequences.
  • Translated protein modification sites to genomic coordinates and constructed the g2pDB database.
  • Implemented a RESTful API for data accessibility.

Main Results:

  • Generated a map of reproducible PTMs across the human proteome.
  • Established direct mapping from protein modification sites to genomic codon locations.
  • Developed g2pDB, a database integrating PTM and genomic data.
  • Created an API to query the impact of nucleotide variants on protein modifications.

Conclusions:

  • g2pDB provides a valuable resource for researchers studying the impact of genetic variation on PTMs.
  • The database facilitates understanding how DNA/RNA variants perturb protein function through PTMs.
  • This work bridges the gap between genomic variation and functional proteomics.