EPIC-DB

A proteomics database for studying Apicomplexan organisms

Carlos J. Madrid-Aliste, Joseph M. Dybas, Ruth Hogue Angeletti, Louis M. Weiss, Kami Kim, I. Simon, Andras Fiser

Research output: Contribution to journalArticle

21 Citations (Scopus)

Abstract

Background: High throughput proteomics experiments are useful for analyzing the protein expression of an organism, identifying the correct gene structure of a genome, or locating possible post-translational modifications within proteins. High throughput methods necessitate publicly accessible and easily queried databases for efficiently and logically storing, displaying, and analyzing the large volume of data. Description: EPICDB is a publicly accessible, queryable, relational database that organizes and displays experimental, high throughput proteomics data for Toxoplasma gondii and Cryptosporidium parvum. Along with detailed information on mass spectrometry experiments, the database also provides antibody experimental results and analysis of functional annotations, comparative genomics, and aligned expressed sequence tag (EST) and genomic open reading frame (ORF) sequences. The database contains all available alternative gene datasets for each organism, which comprises a complete theoretical proteome for the respective organism, and all data is referenced to these sequences. The database is structured around clusters of protein sequences, which allows for the evaluation of redundancy, protein prediction discrepancies, and possible splice variants. The database can be expanded to include genomes of other organisms for which proteome-wide experimental data are available. Conclusion: EPICDB is a comprehensive database of genome-wide T. gondiiand C. parvum proteomics data and incorporates many features that allow for the analysis of the entire proteomes and/or annotation of specific protein sequences. EPICDB is complementary to other -genomics- databases of these organisms by offering complete mass spectrometry analysis on a comprehensive set of all available protein sequences.

Original languageEnglish
Article number38
JournalBMC Genomics
Volume10
DOIs
Publication statusPublished - Jan 21 2009

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Proteomics
Databases
Proteome
Cryptosporidium parvum
Genome
Genomics
Mass Spectrometry
Proteins
Molecular Sequence Annotation
Expressed Sequence Tags
Toxoplasma
Post Translational Protein Processing
Open Reading Frames
Genes
Antibodies

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Madrid-Aliste, C. J., Dybas, J. M., Angeletti, R. H., Weiss, L. M., Kim, K., Simon, I., & Fiser, A. (2009). EPIC-DB: A proteomics database for studying Apicomplexan organisms. BMC Genomics, 10, [38]. https://doi.org/10.1186/1471-2164-10-38

EPIC-DB : A proteomics database for studying Apicomplexan organisms. / Madrid-Aliste, Carlos J.; Dybas, Joseph M.; Angeletti, Ruth Hogue; Weiss, Louis M.; Kim, Kami; Simon, I.; Fiser, Andras.

In: BMC Genomics, Vol. 10, 38, 21.01.2009.

Research output: Contribution to journalArticle

Madrid-Aliste, CJ, Dybas, JM, Angeletti, RH, Weiss, LM, Kim, K, Simon, I & Fiser, A 2009, 'EPIC-DB: A proteomics database for studying Apicomplexan organisms', BMC Genomics, vol. 10, 38. https://doi.org/10.1186/1471-2164-10-38
Madrid-Aliste CJ, Dybas JM, Angeletti RH, Weiss LM, Kim K, Simon I et al. EPIC-DB: A proteomics database for studying Apicomplexan organisms. BMC Genomics. 2009 Jan 21;10. 38. https://doi.org/10.1186/1471-2164-10-38
Madrid-Aliste, Carlos J. ; Dybas, Joseph M. ; Angeletti, Ruth Hogue ; Weiss, Louis M. ; Kim, Kami ; Simon, I. ; Fiser, Andras. / EPIC-DB : A proteomics database for studying Apicomplexan organisms. In: BMC Genomics. 2009 ; Vol. 10.
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