Abstract:
:This year's Database Issue of Nucleic Acids Research contains 152 papers that include descriptions of 54 new databases and update papers on 98 databases, of which 16 have not been previously featured in NAR As always, these databases cover a broad range of molecular biology subjects, including genome structure, gene expression and its regulation, proteins, protein domains, and protein-protein interactions. Following the recent trend, an increasing number of new and established databases deal with the issues of human health, from cancer-causing mutations to drugs and drug targets. In accordance with this trend, three recently compiled databases that have been selected by NAR reviewers and editors as 'breakthrough' contributions, denovo-db, the Monarch Initiative, and Open Targets, cover human de novo gene variants, disease-related phenotypes in model organisms, and a bioinformatics platform for therapeutic target identification and validation, respectively. We expect these databases to attract the attention of numerous researchers working in various areas of genetics and genomics. Looking back at the past 12 years, we present here the 'golden set' of databases that have consistently served as authoritative, comprehensive, and convenient data resources widely used by the entire community and offer some lessons on what makes a successful database. The Database Issue is freely available online at the https://academic.oup.com/nar web site. An updated version of the NAR Molecular Biology Database Collection is available at http://www.oxfordjournals.org/nar/database/a/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Galperin MY,Fernández-Suárez XM,Rigden DJdoi
10.1093/nar/gkw1188subject
Has Abstractpub_date
2017-01-04 00:00:00pages
D1-D11issue
D1eissn
0305-1048issn
1362-4962pii
gkw1188journal_volume
45pub_type
abstract::Module identification is a frequently used approach for mining local structures with more significance in global networks. Recently, a wide variety of bilayer networks are emerging to characterize the more complex biological processes. In the light of special topological properties of bilayer networks and the accompan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw679
更新日期:2016-11-16 00:00:00
abstract::DNA polymerase beta (polbeta), a member of the X family of DNA polymerases, is the major polymerase in the base excision repair pathway. Using in vitro selection, we obtained RNA aptamers for polbeta from a variable pool of 8 x 10(12) individual RNA sequences containing 30 random nucleotides. A total of 60 individual ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl326
更新日期:2006-05-17 00:00:00
abstract::Nam8, a component of yeast U1 snRNP, is optional for mitotic growth but required during meiosis, because Nam8 collaborates with Mer1 to promote splicing of essential meiotic mRNAs AMA1, MER2 and MER3. Here, we identify SPO22 and PCH2 as novel targets of Nam8-dependent meiotic splicing. Whereas SPO22 splicing is co-dep...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1328
更新日期:2011-04-01 00:00:00
abstract::Bulky lesions in the template strand block the progression of RNA polymerase II (RNAP II) and are repaired more rapidly than lesions in the non-transcribed strand, which do not block transcription. In order to better understand the basis of this transcription-coupled repair we developed an in vitro system with purifie...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.4.787
更新日期:1997-02-15 00:00:00
abstract::Triethylammonium uridine-3',5'-cyclic phosphorothioate crystallizes in space group P2(1)2(1)2(1), a = 7.177(1), b = 13.155(6), c = 21.114(7) A, C15H26N3O7PS, MW 423.4, Z = 4, dx = 1.41g/cm3. The crystal structure was solved by direct methods on the basis of 1493 counter X-ray diffraction data (CuK alpha) and refined t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.12.4945
更新日期:1987-06-25 00:00:00
abstract::The interaction of RNase T1 with calf thymus DNA was studied using uv difference spectroscopy and the effect of the enzyme on DNA melting. There was no indication of RNase T1 binding with native DNA. A prominent difference spectrum for RNase T1 binding with denatured DNA (d-DNA) was observed at pH 5, 25 degrees and lo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.1.11
更新日期:1975-01-01 00:00:00
abstract::Aging research is a multi-disciplinary field encompassing knowledge from many areas of basic, applied and clinical research. Age-related processes occur on molecular, cellular, tissue, organ, system, organismal and even psychological levels, trigger the onset of multiple debilitating diseases and lead to a loss of fun...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1287
更新日期:2016-01-04 00:00:00
abstract::We have isolated a rat cDNA, named FE65, hybridizing to an mRNA of about 2,300 nucleotides present in rat brain, undetectable in rat liver and very poorly represented in other tissues. An mRNA of the same size is present in human neuroblastoma cells and is absent from other human cell lines. The FE65 cDNA contains an ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.19.5269
更新日期:1991-10-11 00:00:00
abstract::In vitro selection of RNA-cleaving DNAzymes is a powerful method for isolating metal-specific DNA. A few successful examples are known, but it is still difficult to target some thiophilic metals such as Cd(2+) due to limited functional groups in DNA. While using modified bases expands the chemical functionality of DNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv519
更新日期:2015-07-13 00:00:00
abstract::Studying the intricate folding of rRNA within the ribosome remains a complex problem. Phenanthroline-Cu(II) complexes cleave phosphodiester bonds in rRNA in specific regions, apparently especially where the rRNA structure is constrained in some fashion. We have introduced phenanthroline-copper complexes into 50S Esche...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.8.1906
更新日期:1999-04-15 00:00:00
abstract::Arabidopsis microRNA (miRNA) genes (MIR) give rise to 20- to 22-nt miRNAs that are generated predominantly by the type III endoribonuclease Dicer-like 1 (DCL1) but do not require any RNA-dependent RNA Polymerases (RDRs) or RNA Polymerase IV (Pol IV). Here, we identify a novel class of non-conserved MIR genes that give...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq590
更新日期:2010-11-01 00:00:00
abstract::The ProtoNet site provides an automatic hierarchical clustering of the SWISS-PROT protein database. The clustering is based on an all-against-all BLAST similarity search. The similarities' E-score is used to perform a continuous bottom-up clustering process by applying alternative rules for merging clusters. The outco...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg096
更新日期:2003-01-01 00:00:00
abstract::DNA methylation plays critical roles in transcriptional regulation and chromatin remodeling. Differentially methylated regions (DMRs) have important implications for development, aging and diseases. Therefore, genome-wide mapping of DMRs across various temporal and spatial methylomes is important in revealing the impa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr053
更新日期:2011-05-01 00:00:00
abstract::In general, synthetic RNA transcripts corresponding to the 3' ends of Saccharomyces cerevisiae genes appear to be accurately cleaved and polyadenylated in vitro under appropriate conditions in yeast cell extracts. Initially, however, the endpoints observed in vitro for the GAL7 gene failed to correlate adequately with...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.13.3683
更新日期:1991-07-11 00:00:00
abstract::Methods for increasing the transient level of expression of transfected DNA in cultured Drosophila cells have been examined. Here we show that cells exposed to the steroid hormone 20-hydroxyecdysone for 48h prior to transfection show an 4 to 5 fold increase in the levels of expression of transfected DNA. By analysis, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.22.9255
更新日期:1987-11-25 00:00:00
abstract::Conformations of 8-bromo-2'-[unk]-triisopropylbenzenesulfonyladenosine ([unk]) and its 3'-[unk]-isomer ([unk]) in solution have been determined by the use of intramolecular nuclear Overhauser effects in (1)H NMR spectroscopy. Compound [unk] has been proved to have a conformation in which the adenosine and benzene ring...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.6.823
更新日期:1974-06-01 00:00:00
abstract::The cells of the bronchial epithelium of man are targets for benzo(a)pyrene carcinogenesis. When cultures of these cells, and of non-target fibroblasts, are exposed to [3H]-benzo(a)pyrene, we find that the epithelial cells metabolise and bind to DNA far greater amounts of benzpyrene than do fibroblasts. By analysis of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.5.1547
更新日期:1982-03-11 00:00:00
abstract::Analysis of processing, assembly, and function of higher eukaryotic ribosomal RNA (rRNA) has been hindered by the lack of an expression system that enables rRNA to be modified and then examined functionally. Given the potential usefulness of such a system, we have developed one for mammalian 18S rRNA. We inserted a se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks530
更新日期:2012-09-01 00:00:00
abstract::PCAF and hGCN5 are distinct human genes that encode proteins related to the yeast histone acetyltransferase and transcriptional adapter GCN5. The PCAF protein shares extensive similarity with the 439 amino acids of yGCN5, but it has an approximately 350 amino acid N-terminal extension that interacts with the transcrip...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.12.2948
更新日期:1998-06-15 00:00:00
abstract::Three databases that provide data on transcriptional regulation are described. TRANSFAC is a database on transcription factors and their DNA binding sites. TRRD (Transcription Regulatory Region Database) collects information about complete regulatory regions, their regulation properties and architecture. COMPEL compri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.1.265
更新日期:1997-01-01 00:00:00
abstract::Hepatitis C virus (HCV) RNA is recognized and cleaved in vitro by RNase P enzyme near the AUG start codon. Because RNase P identifies transfer RNA (tRNA) precursors, it has been proposed that HCV RNA adopts structural similarities to tRNA. Here, we present experimental evidence of RNase P sensitivity conservation in n...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki290
更新日期:2005-03-08 00:00:00
abstract::We have developed a comprehensive resource devoted to biologists wanting to optimize the use of gene trap clones in their experiments. We have processed 300 602 such clones from both public and private projects to generate 28,199 'UniTraps', i.e. distinct collections of unambiguous insertions at the same subgenic regi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm825
更新日期:2008-01-01 00:00:00
abstract::Comprehensive understanding of structure and recognition properties of regulatory nucleic acid elements in real time and atomic level is highly important to devise efficient therapeutic strategies. Here, we report the establishment of an innovative biophysical platform using a dual-app nucleoside analog, which serves ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz419
更新日期:2019-07-09 00:00:00
abstract::Infection of Escherichia coli by a bacteriophage T4 regA, gene 44 double mutant leads to about a 7-fold increase in the amount of RNA ligase obtained after infection by wild-type phage. Using cells infected by the double mutant, RNA ligase was purified to homogeneity with a 20% yield. Unlike previous preparations of t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.9.3175
更新日期:1977-09-01 00:00:00
abstract::In metazoan cells, only a limited number of mini chromosome maintenance (MCM) complexes are fired during S phase, while the majority remain dormant. Several methods have been used to map replication origins, but such methods cannot identify dormant origins. Herein, we determined MCM7-binding sites in human cells using...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky476
更新日期:2018-07-27 00:00:00
abstract::A novel resource centre for TP53 mutations and mutants has been developed (http://p53.fr). TP53 gene dysfunction can be found in the majority of human cancer types. The potential use of TP53 mutation as a biomarker for clinical studies or exposome analysis has led to the publication of thousands of reports describing ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1033
更新日期:2013-01-01 00:00:00
abstract::Homeodomains appear to be one of the most frequently employed DNA-binding domains in a superfamily of transacting factors. It is likely that during evolution several sub-types of homeodomain have evolved from a common ancestral domain, resulting in distinct but closely related DNA-binding preferences. Here we describe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.7.1202
更新日期:1994-04-11 00:00:00
abstract::We have isolated the poly(A) polymerase (PAP) encoding gene pla1 [for poly(A) polymerase] from the fission yeast Schizosaccharomyces pombe. Protein sequence alignments with other poly(A) polymerases reveal that pla1 is more closely related to Saccharomyces cerevisiae PAP than to bovine PAP. The two yeast poly(A) polym...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.13.2585
更新日期:1996-07-01 00:00:00
abstract::Pathbase is a database that stores images of the abnormal histology associated with spontaneous and induced mutations of both embryonic and adult mice including those produced by transgenesis, targeted mutagenesis and chemical mutagenesis. Images of normal mouse histology and strain-dependent background lesions are al...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh124
更新日期:2004-01-01 00:00:00
abstract::The effects of the treatment of cultured human and simian cells with Cadmium (Cd), a toxic and carcinogenic metal, were first assayed on macromolecular synthesis. It was observed that DNA synthesis was inhibited by Cd concentrations considerably lower than those inhibiting protein and RNA synthesis. Because of the nec...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.10.4211
更新日期:1987-05-26 00:00:00