Abstract:
:ORegAnno is an open-source, open-access database and literature curation system for community-based annotation of experimentally identified DNA regulatory regions, transcription factor binding sites and regulatory variants. The current release comprises 30 145 records curated from 922 publications and describing regulatory sequences for over 3853 genes and 465 transcription factors from 19 species. A new feature called the 'publication queue' allows users to input relevant papers from scientific literature as targets for annotation. The queue contains 4438 gene regulation papers entered by experts and another 54 351 identified by text-mining methods. Users can enter or 'check out' papers from the queue for manual curation using a series of user-friendly annotation pages. A typical record entry consists of species, sequence type, sequence, target gene, binding factor, experimental outcome and one or more lines of experimental evidence. An evidence ontology was developed to describe and categorize these experiments. Records are cross-referenced to Ensembl or Entrez gene identifiers, PubMed and dbSNP and can be visualized in the Ensembl or UCSC genome browsers. All data are freely available through search pages, XML data dumps or web services at: http://www.oreganno.org.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Griffith OL,Montgomery SB,Bernier B,Chu B,Kasaian K,Aerts S,Mahony S,Sleumer MC,Bilenky M,Haeussler M,Griffith M,Gallo SM,Giardine B,Hooghe B,Van Loo P,Blanco E,Ticoll A,Lithwick S,Portales-Casamar E,Donaldson IJ,doi
10.1093/nar/gkm967subject
Has Abstractpub_date
2008-01-01 00:00:00pages
D107-13issue
Database issueeissn
0305-1048issn
1362-4962pii
gkm967journal_volume
36pub_type
杂志文章abstract::We characterize a component of the E. coli bacterial nucleoid H1a, which accumulates in stationary phase. This protein, identical with the major component of a plasmid-protein complex previously isolated in our laboratory, has a pI close to 7.5. Acrylamide gel electrophoresis and sedimentation in sucrose gradient have...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.13.5321
更新日期:1984-07-11 00:00:00
abstract::In 2.5 x 10(-4)M EDTA buffer, the derivative melting curve of calf thymus DNA shows a major band at 47 degrees with a shoulder at about 54 degrees . The fraction of melting area of this shoulder is about 13%. For reconstituted polylysine-calf thymus DNA complexes, in addition to the melting of free DNA regions at abou...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/1.2.257
更新日期:1974-02-01 00:00:00
abstract::Transcription of transfer RNA genes by RNA polymerase III (Pol III) is controlled by general factors, TFIIIB and TFIIIC, and a negative regulator, Maf1. Here we report the interplay between TFIIIC and Maf1 in controlling Pol III activity upon the physiological switch of yeast from fermentation to respiration. TFIIIC d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky656
更新日期:2018-10-12 00:00:00
abstract::siRNAs confer sequence specific and robust silencing of mRNA. By virtue of these properties, siRNAs have become therapeutic candidates for disease intervention. However, their use as therapeutic agents can be hampered by unintended off-target effects by either or both strands of the siRNA duplex. We report here that u...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq961
更新日期:2011-03-01 00:00:00
abstract::Mitochondrial DNA (mtDNA) is entirely dependent on nuclear genes for its transcription and replication. One of these genes is TOP1MT, which encodes the mitochondrial DNA topoisomerase IB, involved in mtDNA relaxation. To elucidate TOP1MT regulation, we performed genome-wide profiling across the 60-cell line panel (the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr208
更新日期:2011-08-01 00:00:00
abstract::We have demonstrated that the DNA sequence between two triplex-forming polypurine.polypyrimidine (Pu.Py) tracts was protected from DNA modifying enzymes upon formation of triplex DNA structures with an oligodeoxyribonucleotide in which two triplex-forming Pu or Py tracts were placed at the termini (triplex-bridge form...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.3.452
更新日期:1995-02-11 00:00:00
abstract::We have previously shown that hedamycin, a GC-rich DNA-binding antitumor agent, downregulates survivin transcription (Wu et al. (2005) Molecular mechanism of inhibition of survivin transcription by the GC-rich sequence selective DNA-binding antitumor agent, hedamycin: evidence of survivin downregulation associated wit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm149
更新日期:2007-01-01 00:00:00
abstract::The Neurospora VS ribozyme is a catalytic RNA that has the unique ability to specifically recognize and cleave a stem-loop substrate through formation of a highly stable kissing-loop interaction (KLI). In order to explore the engineering potential of the VS ribozyme to cleave alternate substrates, we substituted the w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw401
更新日期:2016-08-19 00:00:00
abstract::DNA strand exchange, the central step of homologous recombination, is considered to occur approximately independently of DNA sequence content. However, certain prokaryotic and eukaryotic genomic loci display either an enhanced or reduced frequency of genetic exchange. Here we show that the Homo sapiens DNA strand exch...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl355
更新日期:2006-05-24 00:00:00
abstract::In recent years, the increase in the amounts of available genomic data has made it easier to appreciate the extent by which organisms increase their genetic diversity through horizontally transferred genetic material. Such transfers have the potential to give rise to extremely dynamic genomes where a significant propo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki187
更新日期:2005-02-16 00:00:00
abstract::Infrared spectroscopy was used to identify hydration-sensitive structural differences between single- stranded phosphorothioate (PS) and phosphodiester (PO) oligodeoxyribonucleotides. Spectra were recorded in the mid-infrared region, 500-1800 cm-1, at relative humidities between 0 and 98%; the PS and PO spectra are su...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.16.3261
更新日期:1996-08-15 00:00:00
abstract::We recently developed a new type of pyrrole (Py)-imidazole (Im) polyamide-tetrahydrocyclopropabenzindolone (CBI) conjugate with an indole linker as a stable sequence-specific alkylating agent. In this study, we investigated the gene silencing activities of polyamides A, B and C, which selectively alkylate specific seq...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl005
更新日期:2006-02-25 00:00:00
abstract::U1-snRNA is an integral part of the U1 ribonucleoprotein pivotal for pre-mRNA splicing. Toll-like receptor (TLR) signaling has recently been associated with immunoregulatory capacities of U1-snRNA. Using lung A549 epithelial/carcinoma cells, we report for the first time on interferon regulatory factor (IRF)-3 activati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp525
更新日期:2009-08-01 00:00:00
abstract::Array based DNA pooling techniques facilitate genome-wide scale genotyping of large samples. We describe a structured analysis method for pooled data using internal replication information in large scale genotyping sets. The method takes advantage of information from single nucleotide polymorphisms (SNPs) typed in par...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl136
更新日期:2006-04-20 00:00:00
abstract::The 5'-flanking region of the bovine prolactin gene was cloned and sequenced. The expression of chimeric gene constructs containing 5'-flanking DNA fragments from the prolactin gene joined to a reporter gene encoding human growth hormone (hGH) was examined using transiently transfected rat pituitary cells. Prolactin n...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:
更新日期:1990-08-25 00:00:00
abstract::LINKER was developed as an online server to assist biomedical researchers to design linker sequences for constructing functional fusion proteins. The program automatically generates a set of peptide sequences that are known to adopt extended conformations as determined by X-ray crystallography and NMR. In addition to ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh422
更新日期:2004-07-01 00:00:00
abstract::Many RNP proteins contain one or more copies of the RNA recognition motif (RRM) and are thought to be involved in cellular RNA metabolism. We have previously characterized in Xenopus a nervous system specific gene, nrp1, that is more similar to the hnRNP A/B proteins than to other known proteins (K. Richter, P. J. Goo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.4.999
更新日期:1993-02-25 00:00:00
abstract::In diverse bacterial species, the turnover and processing of many RNAs is mediated by the ribonuclease RNase J, a member of the widely occurring metallo-β-lactamase enzyme family. We present crystal structures of Streptomyces coelicolor RNase J with bound RNA in pre- and post-cleavage states, at 2.27 Å and 2.80 Å reso...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv732
更新日期:2015-09-18 00:00:00
abstract::Ribosomal protein (RP) genes must be coordinately expressed for proper assembly of the ribosome yet the mechanisms that control expression of RP genes in metazoans are poorly understood. Recently, TATA-binding protein-related factor 2 (TRF2) rather than the TATA-binding protein (TBP) was found to function in transcrip...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx676
更新日期:2017-10-13 00:00:00
abstract::The dissection of RNA editing mechanisms in PHYSARUM: mitochondria has been hindered by the absence of a soluble in vitro system. Based on our studies in isolated mitochondria, insertion of non-encoded nucleotides into PHYSARUM: mitochondrial RNAs is closely linked to transcription. Here we have fractionated mitochond...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.19.3695
更新日期:2000-10-01 00:00:00
abstract::An important model system for studying the process leading to productive transcription is provided by the superfamily of nuclear receptors, which are for the most part ligand-controlled transcription factors. Over the past years several 'orphan' nuclear receptors have been isolated for which no ligand has yet been ide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.16.3424
更新日期:2001-08-15 00:00:00
abstract::Synthesis of (p)ppRNA-DNA chains by purified HeLa cell DNA primase-DNA polymerase alpha (pol alpha-primase) was compared with those synthesized by a multiprotein form of DNA polymerase alpha (pol alpha 2) using unique single-stranded DNA templates containing the origin of replication for simian virus 40 (SV40) DNA. Th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.18.7305
更新日期:1986-09-25 00:00:00
abstract::A feature of Haemophilus influenzae genomes is the presence of several loci containing tracts of six or more identical tetranucleotide repeat units. These repeat tracts are unstable and mediate high frequency, reversible alterations in the expression of surface antigens. This process, termed phase variation (PV), enab...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki180
更新日期:2005-01-14 00:00:00
abstract::Loading of the replicative ring helicase onto the origin of replication (oriC) is the final outcome of a well coordinated series of events that collectively constitute a primosomal cascade. Once the ring helicase is loaded, it recruits the primase and signals the switch to the polymerization mode. The transient nature...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh628
更新日期:2004-06-01 00:00:00
abstract::The human 7SL RNA component of the signal recognition particle can be separated into four major conformers by nondenaturing polyacrylamide gel electrophoresis. We have investigated what sequences give 7SL RNA the property to exist in different conformations. The human 7SL gene 7L30.1 was mutagenized using the random l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.11.4639
更新日期:1986-06-11 00:00:00
abstract::Many interacting proteins regulate and/or assist the activities of RAD51, a recombinase which plays a critical role in both DNA repair and meiotic recombination. Yeast two-hybrid screening of a human testis cDNA library revealed a new protein, RAD51AP2 (RAD51 Associated Protein 2), that interacts strongly with RAD51. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl665
更新日期:2006-01-01 00:00:00
abstract::The hybridization of complementary strands of DNA is the underlying principle of all microarray-based techniques for the analysis of DNA variation. In this paper, we study how probe immobilization at surfaces, specifically probe density, influences the kinetics of target capture using surface plasmon resonance (SPR) s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.24.5163
更新日期:2001-12-15 00:00:00
abstract::The model mRNA (MR), 11-mer RNA containing two nitroxide spin labels at the 5'- and 3'-terminal nucleotides and prone to form a stable homodimer (MR)2, was used for Electron Paramagnetic Resonance study of structural rearrangements in mRNA occurring upon its binding to human 80S ribosomes. The formation of two differe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1136
更新日期:2018-01-25 00:00:00
abstract::In a recent paper we have estimated the total number of protein coding open reading frames (ORFs) in the Saccharomyces cerevisiae genome, based on their properties, at about 4800. This number is much smaller than the 5800-6000 which is widely accepted. In this paper we analyse differences between the set of ORFs with ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.17.3503
更新日期:1999-09-01 00:00:00
abstract::Prior work has indicated that an octanucleotide [5'TATAAGTA(+1)3'] sequence is used as a promoter in yeast mitochondria. Two such sequences (FP1 and FP2) are present upstream of the tRNA(fMet)-RNAse P RNA -tRNA(Pro) gene cluster but only the FP1 promoter but not the FP2 appears to be active in vivo and in vitro. The r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.21.5937
更新日期:1991-11-11 00:00:00