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PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease
2007
Nucleic Acids Research
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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 ...
PeroxisomeDB is structured in interrelated sections 'Genes', 'Functions', 'Metabolic pathways' and 'Diseases', that include hyperlinks to selected features of NCBI, ENSEMBL and UCSC databases. ...
A.S. was a fellow of the AFM, Decrypthon Program and a recipient of FIS (CA05/0090) from the Instituto de Salud Carlos III. ...
doi:10.1093/nar/gkl935
pmid:17135190
pmcid:PMC1747181
fatcat:65vgd4cd3zgkbdgadn7mdcyt4u
PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome
2009
Nucleic Acids Research
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The previous PeroxisomeDB version organized the peroxisomal proteome of humans and Saccharomyces cerevisiae based on genetic and functional information into metabolic categories with a special focus on ...
PeroxisomeDB 2.0 is a freely available, highly interactive functional genomics platform that offers an extensive view on the peroxisomal metabolome across lineages, thus facilitating comparative genomics ...
ACKNOWLEDGEMENTS The authors gratefully acknowledge the computer resources, technical expertise and assistance provided by the Barcelona Supercomputing Center-Centro Nacional de Supercomputacio´n, and ...
doi:10.1093/nar/gkp935
pmid:19892824
pmcid:PMC2808949
fatcat:6jefkejbbbgqtgdrqgb3ew6qmy
OPA3, mutated in 3-methylglutaconic aciduria type III, encodes two transcripts targeted primarily to mitochondria
2010
Molecular Genetics and Metabolism
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OPA3 protein function remains unknown, but it contains a putative mitochondrial leader sequence, mitochondrial sorting signal and a peroxisomal sorting signal. ...
These findings thus place the cellular metabolic defect of 3-MGCA type III in the mitochondrion rather than the peroxisome and implicate loss of OPA3A rather than gain of OPA3B in disease etiology. ...
This study was supported by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA and by the Costeff Support Group Foundation ...
doi:10.1016/j.ymgme.2010.03.005
pmid:20350831
pmcid:PMC2872056
fatcat:rup3of7ajnfkvnoyw7aensrviy
Computational Methods for the Study of Peroxisomes in Health and Disease
[chapter]
2022
Physiology
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Here, we intend to provide an overview of advanced computational methods for the analysis of imaging data, protein structure modeling, proteomics, and genomics. ...
This chapter may serve as a broad resource for the current status of technological advances, and an introduction to computational methods for peroxisome research. ...
Computational Methods for the Study of Peroxisomes in Health and Disease DOI: http://dx.doi.org/10.5772/intechopen.103178 ...
doi:10.5772/intechopen.103178
fatcat:k7kktnbe5ncarmb6ka5q7zgpa4
Accounting for Protein Subcellular Localization: A Compartmental Map of the Rat Liver Proteome
2016
Molecular & Cellular Proteomics
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The Peroxisome Database (32) (peroxisomeDB) is a catalog of the peroxisomal proteome of multiple species, including rat, compiled from experimental literature review, homology and bioinformatic annotation ...
Fifty-eight rat proteins in the peroxisomeDB were present in the Prolocate high stringency data set and a majority were assigned a primary peroxisomal localization. ...
The authors declare no competing financial interests. ...
doi:10.1074/mcp.m116.064527
pmid:27923875
pmcid:PMC5294208
fatcat:qosiftgukfhktjyu4ycqn5tlfy
Transcriptomic Profiling of Peroxisome-related Genes Reveals a Novel Prognostic Signature in Hepatocellular Carcinoma
2020
Genes and Diseases
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Emerging evidence suggests that peroxisomes play a role in the regulation of tumorigenesis and cancer progression. ...
First, univariate Cox regression analysis was employed to identify prognostic peroxisome-related genes in The Cancer Genome Atlas liver cancer cohort, and least absolute shrinkage and selection operator ...
Genomes (KEGG) database, 23 a well-known database for genes and pathways; and protein-coding genes from the proteome of human liver peroxisomes (60 genes). 24 In total, 113 nonredundant peroxisome-related ...
doi:10.1016/j.gendis.2020.04.010
pmid:35005112
pmcid:PMC8720664
fatcat:hhpylh6hgvaxrihzh6l4bdi3gm
A Global Analysis of Enzyme Compartmentalization to Glycosomes
2020
Pathogens
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These include diverse monoxenous species and dixenous species with very different hosts. For many of these, genome or transcriptome sequences are available. ...
This organelle shares a common ancestor with the better-understood eukaryotic peroxisome. ...
Acknowledgments: This work and part of the publication costs were supported by University of Minnesota ...
doi:10.3390/pathogens9040281
pmid:32290588
pmcid:PMC7237986
fatcat:735jd2zvzvhcbnumajla4uiirm
BiomarkerDigger: A versatile disease proteome database and analysis platform for the identification of plasma cancer biomarkers
2009
Proteomics
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We have developed a proteome database (DB), BiomarkerDigger (http://biomarkerdigger.org) that automates data analysis, searching, and metadata-gathering function. ...
The metadatagathering function searches proteome DBs for protein-protein interaction, Gene Ontology, protein domain, Online Mendelian Inheritance in Man, and tissue expression profile information and integrates ...
MitoP2 and PeroxisomeDB are designed to provide comprehensive proteome expression information specific for the mitochondria and the peroxisomes, respectively. ...
doi:10.1002/pmic.200800593
pmid:19639590
fatcat:6ents4sdhvg5la3plc3cksuje4
Predicted mouse peroxisome-targeted proteins and their actual subcellular locations
2008
BMC Bioinformatics
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Conclusion: In a few cases the PTS may oscillate from "silent" to "functional" depending on its surface accessibility indicating the potential for context-dependent conditional subcellular sorting. ...
For rapid confirmation of five new PTS2-and two previously identified PTS1-containing candidates we developed the new cell line CHO-perRed which stably expresses the peroxisomal marker dsRed-PTS1. ...
Acknowledgements We thank Mitsunori Fukuda for providing plasmids. We are grateful to Ken Yagi, Yosuke Mizuno and Yutaka Nakachi for helpful discussions. ...
doi:10.1186/1471-2105-9-s12-s16
pmid:19091015
pmcid:PMC2638156
fatcat:fldmyskr7readl6dadxog6xgzy
Anaerobic peroxisomes in Entamoeba histolytica metabolize myo-inositol
2021
PLoS Pathogens
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The presence of peroxisomes in E. histolytica and other archamoebae breaks the paradigm of peroxisome absence in anaerobes and provides a new potential target for the development of antiparasitic drugs ...
Proteomic analyses of affinity-purified peroxisomes and in silico PTS1 predictions provided datasets of 655 and 56 peroxisomal candidates, respectively; however, only six proteins were shared by both datasets ...
Acknowledgments The authors wish to thank Michaela Marcinčikova ´for her excellent technical assistance, and Marie Ols ˇinova ´for her help with fluorescence microscopy. ...
doi:10.1371/journal.ppat.1010041
pmid:34780573
pmcid:PMC8629394
fatcat:hd7npujmgrafhbgsz3kz5z3zam
Peroxisome Biogenesis and Function
2009
The Arabidopsis Book
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Genetic and functional information about known peroxisomal proteins of Homo sapiens (85 proteins) and Saccharomyces (61 proteins) can be found in the database PeroxisomeDB (www.peroxisomedb.org; Schluter ...
disease, which result from defects in peroxisome function or formation. ...
ACKNOWLEDGMENTS We are grateful to Gregg Howe for critical reading of the JA biosynthesis section, and Karen Bird for editorial assistance.
REFERENCES CITED ...
doi:10.1199/tab.0123
pmid:22303249
pmcid:PMC3243405
fatcat:ykz4xdawtzahzc75nwygkafs5q
Two novel compound heterozygous mutations in OPA3 in two siblings with OPA3-related 3-methylglutaconic aciduria
2014
Molecular Genetics and Metabolism Reports
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for a mitochondrial pathology in this disease. ...
Thus, though the exact function of OPA3 remains unknown, our experimental results and clinical summary provide evidence for the pathogenicity of the identified OPA3 variants and provide further evidence ...
Acknowledgments This study was supported by the Intramural Research Program of the National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA. ...
doi:10.1016/j.ymgmr.2014.02.003
pmid:24749080
pmcid:PMC3987911
fatcat:eag7p5xxcbbejimxccd4s4xq2q
Reduced peroxisomal import triggers peroxisomal retrograde signaling
2021
Cell Reports
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Using proteomic and transcriptomic analyses, we show that proteins involved in peroxisomal lipid metabolism and immunity are also upregulated upon prx-5(RNAi). ...
Using Caenorhabditis elegans, we present evidence of the existence of such retrograde signaling for peroxisomes, which we define as the peroxisomal retrograde signaling (PRS). ...
INTRODUCTION Various human diseases, for example Refsum's disease or X-linked adrenoleukodystrophy, are associated with disrupted fatty acid metabolism. ...
doi:10.1016/j.celrep.2020.108653
pmid:33472070
fatcat:4ftapf5yufd7rhxfurlmmutgia
Classification of Subcellular Location by Comparative Proteomic Analysis of Native and Density-shifted Lysosomes
2011
Molecular & Cellular Proteomics
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One approach to the functional characterization of the lysosome lies in the use of proteomic methods to identify proteins in subcellular fractions enriched for this organelle. ...
These results establish a quanti-tative mass spectrometric/subcellular fractionation approach for identification of lysosomal proteins and underscore the necessity of balance sheet analysis for localization ...
All mgf files from the MALDI-TOF/TOF experiments were merged and used to search a combined database consisting of the ENSEMBL rat and mouse proteomes (Rattus_norvegicus.RGSC3.4.58.pep.all and Mus_musculus.NCBIM37.58 ...
doi:10.1074/mcp.m110.006403
pmid:21252268
pmcid:PMC3069348
fatcat:qplgxmxai5gqznfqxahaqwl3x4
A novel USP30 inhibitor recapitulates genetic loss of USP30 and sets the trigger for PINK1-PARKIN amplification of mitochondrial ubiquitylation
[article]
2020
bioRxiv
pre-print
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It has been proposed as an actionable target to alleviate the loss of function of the mitophagy pathway governed by the Parkinsons Disease associated genes PINK1 and PRKN. ...
We demonstrate that ubiquitylation of TOM20, a component of the outer mitochondrial membrane import machinery that directly interacts with USP30, represents a robust biomarker for both USP30 loss and inhibition ...
Funding for ODDI was obtained by John Davis. We thank Jon Lane and Ian Ganley for provision of cell lines. ...
doi:10.1101/2020.04.16.044206
fatcat:p6a4mr4dfzdutev3ge2v5iban4
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