title: PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.
abstract: 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.
authors.affiliation: 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.
authors.forename: Agatha
authors.initials: A
authors.lastname: Schlüter
authors.forename: Stéphane
authors.initials: S
authors.lastname: Fourcade
authors.forename: Enric
authors.initials: E
authors.lastname: Domènech-Estévez
authors.forename: Toni
authors.initials: T
authors.lastname: Gabaldón
authors.forename: Jaime
authors.initials: J
authors.lastname: Huerta-Cepas
authors.forename: Guillaume
authors.initials: G
authors.lastname: Berthommier
authors.forename: Raymond
authors.initials: R
authors.lastname: Ripp
authors.forename: Ronald J A
authors.initials: RJ
authors.lastname: Wanders
authors.forename: Olivier
authors.initials: O
authors.lastname: Poch
authors.forename: Aurora
authors.initials: A
authors.lastname: Pujol
mesh_terms: D000818:Animals; D030562:Databases, Protein; D023281:Genomics; D006801:Humans; D020407:Internet; D051379:Mice; D018901:Peroxisomal Disorders / Q000235:genetics*; D020675:Peroxisomes / Q000378:metabolism*; D021382:Protein Sorting Signals; D020543:Proteome / Q000737:chemistry / Q000235:genetics* / Q000502:physiology*; D051381:Rats; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics / Q000502:physiology; D012984:Software; D014584:User-Computer Interface
chemical_list: D021382:Protein Sorting Signals; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins