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Related Concept Videos

Diversity of Protists II01:27

Diversity of Protists II

Alveolates are a group of organisms recognized by the presence of alveoli, which are cytoplasmic sacs located beneath the cell membrane. While their function remains uncertain, alveoli may help regulate water balance by controlling how much water enters and leaves the cell. In dinoflagellates, these structures may serve as armor plates. There are three major types of alveolates: ciliates, which move using cilia; dinoflagellates, which use flagella for movement; and apicomplexans, which are...
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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.
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EPIC-DB: a proteomics database for studying Apicomplexan organisms.

Carlos J Madrid-Aliste1, Joseph M Dybas, Ruth Hogue Angeletti

  • 1Biodefense Proteomics Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA. cmadrid@fiserlab.org

BMC Genomics
|January 23, 2009
PubMed
Summary
This summary is machine-generated.

EPICDB is a new database for high-throughput proteomics data from Toxoplasma gondii and Cryptosporidium parvum. It provides a centralized resource for mass spectrometry and antibody experimental results, aiding in gene and protein analysis.

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Genomics

Background:

  • High-throughput proteomics generates vast datasets requiring efficient storage and analysis.
  • Publicly accessible databases are crucial for managing and interpreting large-scale biological data.

Purpose of the Study:

  • To introduce EPICDB, a novel relational database for high-throughput proteomics data.
  • To provide a queryable resource for experimental proteomics data of Toxoplasma gondii and Cryptosporidium parvum.

Main Methods:

  • Developed a publicly accessible, queryable relational database (EPICDB).
  • Integrated mass spectrometry and antibody experimental data.
  • Incorporated functional annotations, comparative genomics, and sequence alignments (ESTs, ORFs).
  • Structured data around protein sequence clusters to evaluate redundancy and splice variants.

Main Results:

  • EPICDB organizes and displays comprehensive proteomics data for T. gondii and C. parvum.
  • The database includes all available alternative gene datasets, forming a complete theoretical proteome.
  • Data is referenced to these sequences, enabling analysis of redundancy and discrepancies.

Conclusions:

  • EPICDB is a comprehensive resource for genome-wide proteomics data of T. gondii and C. parvum.
  • The database facilitates analysis of entire proteomes and specific protein sequences.
  • EPICDB complements existing genomics databases by providing detailed mass spectrometry analysis.