PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease

Peroxisomes are essential organelles of eukaryotic origin, ubiquitously distributed in cells and organisms, playing key roles in lipid and antioxidant metabolism. Loss or malfunction of peroxisomes causes more than 20 fatal inherited conditions. We have created a peroxisomal database (http://www.per...

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Bibliographic Details
Published in:Nucleic acids research 2007-01, Vol.35 (suppl-1), p.D815-D822
Main Authors: Schlüter, Agatha, Fourcade, Stéphane, Domènech-Estévez, Enric, Gabaldón, Toni, Huerta-Cepas, Jaime, Berthommier, Guillaume, Ripp, Raymond, Wanders, Ronald J.A, Poch, Olivier, Pujol, Aurora
Format: Article
Language:English
Subjects:
Animals
Biochemistry, Molecular Biology
Databases, Protein
Genomics
Humans
Internet
Life Sciences
Mice
Molecular biology
Peroxisomal Disorders
Peroxisomal Disorders - genetics
Peroxisomes
Peroxisomes - metabolism
Protein Sorting Signals
Proteome
Proteome - chemistry
Proteome - genetics
Proteome - physiology
Rats
Saccharomyces cerevisiae
Saccharomyces cerevisiae Proteins
Saccharomyces cerevisiae Proteins - genetics
Saccharomyces cerevisiae Proteins - physiology
Software
User-Computer Interface
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Summary:Peroxisomes are essential organelles of eukaryotic origin, ubiquitously distributed in cells and organisms, playing key roles in lipid and antioxidant metabolism. Loss or malfunction of peroxisomes causes more than 20 fatal inherited conditions. We have created a peroxisomal database (http://www.peroxisomeDB.org) that includes the complete peroxisomal proteome of Homo sapiens and Saccharomyces cerevisiae, by gathering, updating and integrating the available genetic and functional information on peroxisomal genes. PeroxisomeDB is structured in interrelated sections 'Genes', 'Functions', 'Metabolic pathways' and 'Diseases', that include hyperlinks to selected features of NCBI, ENSEMBL and UCSC databases. We have designed graphical depictions of the main peroxisomal metabolic routes and have included updated flow charts for diagnosis. Precomputed BLAST, PSI-BLAST, multiple sequence alignment (MUSCLE) and phylogenetic trees are provided to assist in direct multispecies comparison to study evolutionary conserved functions and pathways. Highlights of the PeroxisomeDB include new tools developed for facilitating (i) identification of novel peroxisomal proteins, by means of identifying proteins carrying peroxisome targeting signal (PTS) motifs, (ii) detection of peroxisomes in silico, particularly useful for screening the deluge of newly sequenced genomes. PeroxisomeDB should contribute to the systematic characterization of the peroxisomal proteome and facilitate system biology approaches on the organelle.
ISSN:0305-1048
1362-4962
DOI:10.1093/nar/gkl935