Abstract：
:The Nucleolar Proteome Database (NOPdb) archives data on >700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli, the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene, its domain structures and relevant protein homologues across species, as well as documenting its MS identification history including all the peptides sequenced by tandem MS/MS. Moreover, data showing the quantitative changes in the relative levels of approximately 500 nucleolar proteins are compared at different timepoints upon transcriptional inhibition. Correlating changes in protein abundance at multiple timepoints, highlighted by visualization means in the NOPdb, provides clues regarding the potential interactions and relationships between nucleolar proteins and thereby suggests putative functions for factors within the 30% of the proteome which comprises novel/uncharacterized proteins. The NOPdb (http://www.lamondlab.com/NOPdb) is searchable by either gene names, nucleotide or protein sequences, Gene Ontology terms or motifs, or by limiting the range for isoelectric points and/or molecular weights and links to other databases (e.g. LocusLink, OMIM and PubMed).
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Leung AK,Trinkle-Mulcahy L,Lam YW,Andersen JS,Mann M,Lamond AIdoi
10.1093/nar/gkj004keywords:
subject
Has Abstractpub_date
2006-01-01 00:00:00pages
D218-20issue
Database issueeissn
0305-1048issn
1362-4962pii
34/suppl_1/D218journal_volume
34pub_type
杂志文章abstract：:A cDNA (2855 nt) encoding a putative cytotoxic ribonuclease (rapLR1) related to the antitumor protein onconase was cloned from a library derived from the liver of gravid female amphibian Rana pipiens. The cDNA was mainly comprised (83%) of 3' untranslated region (UTR). Secondary structure analysis predicted two unusua...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.12.2375
更新日期：2000-06-15 00:00:00
abstract：:Assessment of the fidelity of gene expression is crucial to understand cell homeostasis. Here we present a highly sensitive method for the systematic Quantification of Rare Amino acid Substitutions (QRAS) using absolute quantification by targeted mass spectrometry after chromatographic enrichment of peptides with miss...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1319
更新日期：2019-04-08 00:00:00
abstract：:Micrococcal nuclease has been shown to preferentially cleave chromatin in the region of genes actively engaged in transcription. We have used this preferential cleavage to show that the metallothionein (MT) gene in adult mouse liver, when induced to produce mRNA by injection of cadmium, becomes more susceptible to nuc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.10.3255
更新日期：1983-05-25 00:00:00
abstract：:Remodelling protein nucleic acid interfaces is an important biological task, which is often carried out by nucleic acid stimulated ATPases of the Swi2/Snf2 superfamily. Here we study the mechano-chemical cycle of such an ATPase, namely the catalytic domain of the Sulfolobus solfataricus Rad54 homologue (SsoRad54cd), b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn040
更新日期：2008-04-01 00:00:00
abstract：:Chloroplast DNA, isolated from a synchronized culture of Chlamydomonas reinhardii, was digested with restriction endonucleases and examined in the electron microscope. Restriction fragments containing displacement loops (D-loop) were photographed and measured to determine the position of replicated sequences in relati...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.9.3843
更新日期：1984-05-11 00:00:00
abstract：:The biogenesis of ribosomes in vivo is an essential process for cellular functions. Transcription of ribosomal RNA (rRNA) genes is the rate-limiting step in ribosome biogenesis controlled by environmental conditions. Here, we investigated the role of folate antagonist on changes of DNA double-strand breaks (DSBs) land...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw1208
更新日期：2017-03-17 00:00:00
abstract：:IHF and HU are two heterodimeric nucleoid-associated proteins (NAP) that belong to the same protein family but interact differently with the DNA. IHF is a sequence-specific DNA-binding protein that bends the DNA by over 160°. HU is the most conserved NAP, which binds non-specifically to duplex DNA with a particular pr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1236
更新日期：2012-04-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.23.6247
更新日期：1992-12-11 00:00:00
abstract：:A non-enzymic protein factor that increases the in vitro rate of synthesis by HeLa DNA polymerase alpha 15- to 30-fold with denatured DNA as template has been partially purified from the cytoplasmic fraction of HeLa cells. The stimulatory effect is highly specific for HeLa DNA polymerase alpha and for DNA templates th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.1.221
更新日期：1978-01-01 00:00:00
abstract：:A modification of previously described methods of electron microscopic gene mapping and of gene enrichment based on the avidin-biotin interaction is presented. The modification consists of coupling cytochrome-c instead of pentane diamine to the oxidized 2', 3' terminus of an RNA by Schiff base formation and BH-4 reduc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.2.385
更新日期：1978-02-01 00:00:00
abstract：:An 11 S ribonucleoprotein particle was isolated from maize endosperm and shown to be functionally and structurally equivalent to the mammalian signal recognition particle. However, unlike animal cells which apparently contain a single 7 SL RNA species, maize endosperm contains a heterogeneous population of 7 SL RNA. T...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.4.1573
更新日期：1989-02-25 00:00:00
abstract：:CDK12 (cyclin-dependent kinase 12) is a regulatory kinase with evolutionarily conserved roles in modulating transcription elongation. Recent tumor genome studies of breast and ovarian cancers highlighted recurrent CDK12 mutations, which have been shown to disrupt DNA repair in cell-based assays. In breast cancers, CDK...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx187
更新日期：2017-06-20 00:00:00
abstract：:In order to investigate the possible role of RNA secondary structure in determining the efficiency and specificity of mRNA splicing, the structures of sequences at three acceptor splice sites in adenovirus were studied. Transcripts spanning intron-exon junctions were synthesized using SP6 RNA polymerase and analyzed u...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.22.8437
更新日期：1984-11-26 00:00:00
abstract：:The apolipoprotein AI (apoAI) promoter/enhancer contains multiple cis -acting elements on which a variety of hepatocyte-enriched and ubiquitous transcription factors function synergistically to regulate liver-specific transcription. Adenovirus E1A proteins repress tissue-specific gene expression and disrupt the differ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.7.1761
更新日期：1998-04-01 00:00:00
abstract：:Linkage analysis is a successful procedure to associate diseases with specific genomic regions. These regions are often large, containing hundreds of genes, which make experimental methods employed to identify the disease gene arduous and expensive. We present two methods to prioritize candidates for further experimen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl707
更新日期：2006-01-01 00:00:00
abstract：:The Eco57I restriction endonuclease and methylase were purified to homogeneity from the E.coli RR1 strain carrying the eco57IRM genes on a recombinant plasmid. The molecular weight of the denaturated methylase is 63 kDa. The restriction endonuclease exists in a monomeric form with an apparent molecular weight of 104-1...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.22.6043
更新日期：1992-11-25 00:00:00
abstract：:Aberration within the p53 tumor suppressor gene is the most frequently identified genetic damage in human cancer. Regulatory functions proposed for the p53 protein include modulation of the cell cycle, cellular differentiation, signal transduction, and gene expression. Additionally, the p53 gene product may guard the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.3.713
更新日期：1993-02-11 00:00:00
abstract：:It is believed that depending on the thermodynamic stability of the 5'-strand and the 3'-strand in the stem-loop structure of a precursor microRNA (pre-miRNA), cells preferentially select the less stable one (called the miRNA or guide strand) and destroy the other one (called the miRNA* or passenger strand). However, ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm641
更新日期：2007-01-01 00:00:00
abstract：:Synchronous plasmodia of cycloheximide-sensitive and cycloheximide-resistant strains of Physarum polycephalum were labelled with 3[H]-deoxyadenosine in pulse and pulse-chase experiments in presence and absence of cycloheximide. The replication products were studied with alkaline sucrose gradient sedimentation analysis...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.2.405
更新日期：1977-02-01 00:00:00
abstract：:The nucleotide sequence of the chick beta-actin gene was determined. The gene contains 5 introns; 4 interrupt the translated region at codons 41/42, 120/122, 267, 327/328 and a large intron occurs in the 5' untranslated region. The gene has a 97 nucleotide 5'-untranslated region and a 594 nucleotide 3'-untranslated re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.23.8287
更新日期：1983-12-10 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.4.e12
更新日期：2000-02-15 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gng066
更新日期：2003-06-01 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt625
更新日期：2013-10-01 00:00:00
abstract：:Proper expression of the genes of the human beta-globin gene locus requires the associated locus control region (LCR). Structurally, the LCR is defined by the presence of four domains of erythroid-specific chromatin structure. These domains, which have been characterized as DNase I hypersensitive sites (HSs), comprise...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.24.5684
更新日期：1998-12-15 00:00:00
abstract：:To investigate the principles driving recognition between proteins and DNA, we analyzed more than thousand crystal structures of protein/DNA complexes. We classified protein and DNA conformations by structural alphabets, protein blocks [de Brevern, Etchebest and Hazout (2000) (Bayesian probabilistic approach for predi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1273
更新日期：2014-03-01 00:00:00
abstract：:Bovine mitochondrial (mt) phenylalanine tRNA (tRNA(Phe)), which lacks the 'conserved' GG and T psi YCG sequences, was efficiently purified by the selective hybridization method using a solid phase DNA probe. The entire nucleotide sequence of the tRNA, including modified nucleotides, was determined and its higher-order...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.3.347
更新日期：1994-02-11 00:00:00
abstract：:eggNOG is a public database of orthology relationships, gene evolutionary histories and functional annotations. Here, we present version 5.0, featuring a major update of the underlying genome sets, which have been expanded to 4445 representative bacteria and 168 archaea derived from 25 038 genomes, as well as 477 euka...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1085
更新日期：2019-01-08 00:00:00
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journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks671
更新日期：2012-10-01 00:00:00
abstract：:At either end of the nopaline Ti-plasmid T-region resides a copy of a 25 bp repeated element. The normal T-DNA endpoint is 1 bp internal of the right copy, with the transcription initiation site of the nopaline synthase (nos) gene being approximately 300 bp away in the same direction. Here we describe results which de...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.15.6031
更新日期：1984-08-10 00:00:00
abstract：:Myotonic dystrophy type 1 (DM1) is caused by the expansion of a (CTG).(CAG) repeat in the DMPK gene on chromosome 19q13.3. At least 17 neurological diseases have similar genetic mutations, the expansion of DNA repeats. In most of these disorders, the disease severity is related to the length of the repeat expansion, a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh976
更新日期：2004-12-01 00:00:00
