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Nucleic Acids Research Advance Access originally published online on November 28, 2006
Nucleic Acids Research 2007 35(Database issue):D815-D822; doi:10.1093/nar/gkl935
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Nucleic Acids Research, 2007, Vol. 35, Database issue D815-D822
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

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

Agatha Schlüter1, Stéphane Fourcade1, Enric Domènech-Estévez1, Toni Gabaldón2, Jaime Huerta-Cepas2, Guillaume Berthommier3, Raymond Ripp3, Ronald J. A. Wanders4, Olivier Poch3 and Aurora Pujol1,5,*

1 Centre de Genètica Mèdica i Molecular, Institut d'Investigació Biomèdica de Bellvitge-Institut de Recerca Oncològica (IDIBELL-IRO) Hospital Duran i Reynals, Granvia Km 2,7. 08907 Hospitalet de Llobregat, Barcelona, Spain 2 Bioinformatics Department, Centro de Investigación Príncipe Felipe Avda. Autopista del Saler, 16 Valencia 46013, Spain 3 Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP/Collège de France, 1 rue Laurent Fries, BP10142 67404 Illkirch Cedex, France 4 Laboratory of Genetic Metabolic Diseases, Department of Clinical Chemistry and Department of Pediatrics, Emma Children's Hospital, Academic Medical Center, University of Amsterdam PO Box 22700, 1100 DE Amsterdam, The Netherlands 5 Institució Catalana de Recerca i Estudis Avançats (ICREA) Barcelona, Spain

*To whom correspondence should be addressed. Tel: +34 93 2607343; Fax: +34 93 2607414; Email: apujol{at}iro.es

Received August 9, 2006. Revised October 11, 2006. Accepted October 12, 2006.

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.


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