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NOPdb specifications

Information


Unique identifier OMICS_21117
Name NOPdb
Alternative name Nucleolar Proteome Database
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Maintained No

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Publication for Nucleolar Proteome Database

NOPdb citations

 (6)
library_books

Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein Protein Interactions in Intra Nuclear Compartments

2015
Int J Mol Sci
PMCID: 4730271
PMID: 26712748
DOI: 10.3390/ijms17010024

[…] m the intra-nuclear compartment protein database Nsort/DB []. This comprehensive database aggregates data from multiple sources including Nuclear Protein Database (NPD) [], Nuclear Proteome Database (NOPdb) [], Nuclear Matrix Protein Database (NMPdb) [], UniProt [] and Human Protein Reference Database (HPRD) []. The complete nuclear proteome contains 3566 proteins where 1285 proteins are assigned […]

library_books

Mapping the LINE1 ORF1 protein interactome reveals associated inhibitors of human retrotransposition

2013
Nucleic Acids Res
PMCID: 3753637
PMID: 23749060
DOI: 10.1093/nar/gkt512

[…] ransposition of Ty1 and Ty3 yeast Long terminal repeat (LTR) retrotransposons (,). Contrarily, P-body disruption increases retrotransposition of rodent intracisternal A particle (IAP) elements ().The Nucleolar Proteome Database and DAVID reveal that one-half of pc-L1-1FH-associated non-ribosomal proteins can be found in nucleoli (Supplementary Table S6). As with stress granules, a role for nucleol […]

library_books

NOL11, Implicated in the Pathogenesis of North American Indian Childhood Cirrhosis, Is Required for Pre rRNA Transcription and Processing

2012
PLoS Genet
PMCID: 3420923
PMID: 22916032
DOI: 10.1371/journal.pgen.1002892

[…] e majority of the hundreds of nucleolar proteins involved in ribosome biogenesis were first identified in yeast , and were subsequently found in the nucleoli of human cells (http://www.lamondlab.com/NOPdb3.0) . While most of these proteins and their functions are conserved to humans , , it is becoming clear that important differences exist in how ribosome biogenesis is regulated between yeast and […]

call_split

The proteomes of transcription factories containing RNA polymerases I, II or III

2011
Nat Methods
PMCID: 3324775
PMID: 21946667
DOI: 10.1038/nmeth.1705
call_split See protocol

[…] ytoplasm”(GO: 0005737), and 9,682 proteins with the term “nucleus” (GO: 0005634) from the International Protein Index (above), (ii) 4,666 proteins from the nucleolus database http://www.lamondlab.com/NOPdb3.0/), and (iii) 67 “S100” proteins obtained by filtering entries in the Uniprot database (http://www.uniprot.org/) with the key word “S100”. […]

library_books

A Proteomic Screen for Nucleolar SUMO Targets Shows SUMOylation Modulates the Function of Nop5/Nop58

2010
Mol Cell
PMCID: 2938476
PMID: 20797632
DOI: 10.1016/j.molcel.2010.07.025

[…] ntified proteins in either input (data not shown) or eluate (D) samples with the >4500 proteins identified in purified nucleoli () confirmed that most protein groups with high intensity appear in the NopDB (http://www.lamondlab.com/NOPdb3.0/).Histograms (M/L and H/L, E) reveal that log2-ratios are normally distributed due to the lower levels of nucleolar 6HisSUMO-tagged proteins (log2-ratio > 0) a […]

library_books

Identification of Functional Networks of Estrogen and c Myc Responsive Genes and Their Relationship to Response to Tamoxifen Therapy in Breast Cancer

2008
PLoS One
PMCID: 2496892
PMID: 18714337
DOI: 10.1371/journal.pone.0002987

[…] ases of estrogen-responsive genes ((ERGDB, http://research.i2r.a-star.edu.sg/promoter/Ergdb-v11/, ), c-Myc targets (http://www.myc-cancer-gene.org, ), and nucleolar proteins (http://www.lamondlab.com/NOPdb/, current in November 2005. Pathway analysis used Onto-Express (http://vortex.cs.wayne.edu/index.htm, ), Ingenuity Pathways Analysis (Ingenuity Systems, Redwood City, CA, http://www.ingenuity.c […]

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NOPdb institution(s)
Division of Gene Regulation and Expression, Wellcome Trust Biocentre, School of Life Sciences, University of Dundee, Dundee, UK; Department of Biochemistry and Molecular Biology, University of Southern Denmark, Denmark
NOPdb funding source(s)
Supported by a Croucher Foundation Scholarship; Wellcome Trust Principal Research Fellow; The Human Frontier Science Program is acknowledged for a research grant entitled ‘Functional organization of the cell nucleus investigated through proteomics and molecular dynamics; the Wellcome Trust; Danish National Research Foundation grant to the Centre for Experimental Bioinformatics.

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