Abstract:
:Recurrent chromosome aberrations are an important resource when associating human pathologies to specific genes. However, for technical reasons a large number of chromosome breakpoints are defined only at the level of cytobands and many of the genes involved remain unidentified. We developed a web-based information system that mines the scientific literature and generates textual and comprehensive information on all human breakpoints. We show that the statistical analysis of this textual information and its combination with genomic data can identify genes directly involved in DNA rearrangements. The Human Chromosome Aberration Database (HCAD) is publicly accessible at http://www.pdg.cnb.uam.es/UniPub/HCAD/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Hoffmann R,Dopazo J,Cigudosa JC,Valencia Adoi
10.1093/nar/gki061keywords:
subject
Has Abstractpub_date
2005-01-01 00:00:00pages
D511-3issue
Database issueeissn
0305-1048issn
1362-4962pii
33/suppl_1/D511journal_volume
33pub_type
杂志文章abstract::We report the complete DNA sequence of the short repeat region in the genome of herpes simplex virus type 1, as 6633 base pairs of composition 79.5% G+C. This contains immediate early gene 3, encoding the IE175 protein, an important transcriptional activator of later virus genes. The IE175 coding region was identified...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1986-02-25 00:00:00
abstract::Chromosomes in vertebrates are protected at both ends by telomere DNA composed of tandem (TTAGGG)n repeats. DNA replication produces a blunt-ended leading strand telomere and a lagging strand telomere carrying a single-stranded G-rich overhang at its end. The G-rich strand can form G-quadruplex structure in the presen...
journal_title:Nucleic acids research
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doi:10.1093/nar/gkm203
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journal_title:Nucleic acids research
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doi:10.1093/nar/25.11.2189
更新日期:1997-06-01 00:00:00
abstract::New linker phosphoramidite reagents containing a cleavable 3'-ester linkage are used for attaching the first nucleoside to the surface of a solid- phase support. Inexpensive, underivatized amino supports, such as long chain alkylamine controlled-pore glass, can serve as universal supports. No modifications to phosphor...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh222
更新日期:2004-01-29 00:00:00
abstract::The process of strand exchange is considered to be the hallmark of DNA recombination. Proteins known to carry out such exchange are believed to operate via one or the other of two mechanisms. RecA-like proteins promote the formation of a three-stranded or triplex synaptic intermediate in which strand exchange occurs, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.20.4004
更新日期:1997-10-15 00:00:00
abstract::Three Rat1/Xrn2 homologues exist in Arabidopsis thaliana: nuclear AtXRN2 and AtXRN3, and cytoplasmic AtXRN4. The latter has a role in degrading 3' products of miRNA-mediated mRNA cleavage, whereas all three proteins act as endogenous post-transcriptional gene silencing suppressors. Here we show that, similar to yeast ...
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pub_type: 杂志文章
doi:10.1093/nar/gkq172
更新日期:2010-07-01 00:00:00
abstract::The D. melanogaster Adh gene is transcribed from two different promoters; a proximal (larval) promoter is active during late embryonic and larval stages, and a distal (adult) promoter is active primarily in third instar larvae and in adult flies (1). Genetic analyses suggest that several species of the mulleri subgrou...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:1985-10-11 00:00:00
abstract::An unexpectedly high number of regulatory RNAs have been recently discovered that fine-tune the function of genes at all levels of expression. We employed Genomic SELEX, a method to identify protein-binding RNAs encoded in the genome, to search for further regulatory RNAs in Escherichia coli. We used the global regula...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq032
更新日期:2010-06-01 00:00:00
abstract::In this study, we present the DNA-Binding Site Identifier (DBSI), a new structure-based method for predicting protein interaction sites for DNA binding. DBSI was trained and validated on a data set of 263 proteins (TRAIN-263), tested on an independent set of protein-DNA complexes (TEST-206) and data sets of 29 unbound...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt617
更新日期:2013-09-01 00:00:00
abstract::The ASTRAL compendium provides several databases and tools to aid in the analysis of protein structures, particularly through the use of their sequences. It is partially derived from the SCOP database of protein domains, and it includes sequences for each domain as well as other resources useful for studying these seq...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.260
更新日期:2002-01-01 00:00:00
abstract::DNA, isolated from age-synchronous senescent populations of Caenorhabditis elegans has been quantitatively and qualitatively analyzed for the presence of 5-methylcytosine. High performance liquid chromatography on two wild-type and several mutant strains of C. elegans failed to detect any 5-methylcytosine. The restric...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.16.6711
更新日期:1986-08-26 00:00:00
abstract::The A site of the small ribosomal subunit participates in the fidelity of decoding by switching between two states, a resting 'off' state and an active decoding 'on' state. Eight crystal structures of RNA duplexes containing two minimal decoding A sites of the Homo sapiens mitochondrial wild-type, the A1555G mutant or...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn112
更新日期:2008-05-01 00:00:00
abstract::In many eukaryotic mRNAs one or more short 'upstream' open reading frames, uORFs, precede the initiator of the main coding sequence. Upstream ORFs are functionally diverse as illustrated by their variety of features in polyamine pathway biosynthetic mRNAs. Their propensity to act as sensors for regulatory circuits and...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkp1037
更新日期:2010-01-01 00:00:00
abstract::Synthetic biology seeks to envision living cells as a matter of engineering. However, increasing evidence suggests that the genetic load imposed by the incorporation of synthetic devices in a living organism introduces a sort of unpredictability in the design process. As a result, individual part characterization is n...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1280
更新日期:2016-01-08 00:00:00
abstract::Histone modifications are fundamental to chromatin structure and transcriptional regulation, and are recognized by a limited number of protein folds. Among these folds are PHD fingers, which are present in most chromatin modification complexes. To date, about 15 PHD finger domains have been structurally characterized,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq947
更新日期:2011-03-01 00:00:00
abstract::We have examined the ability of a cationic planar chromophore, ethidium bromide, to intercalate into a short, defined triple helix. Using UV absorption, fluorescence spectroscopy and a gel retardation assay we demonstrate that ethidium bromide is able to bind to a triple helix with a lower affinity than to the corresp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.7.1521
更新日期:1991-04-11 00:00:00
abstract::DNA intercalators are found to recognize a DNA lesion as a high affinity receptor site. This lesion-specific binding is observed when one strand of a DNA double helix contains an extra, unpaired nucleotide. Our assay for binding controls for the effects of sequence with a series of oligodeoxynucleotide duplexes which ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.24.11607
更新日期:1988-12-23 00:00:00
abstract::The hexametric T7 helicase (gp4) adopts a spiral lock-washer form and encircles a coil-like DNA (tracking) strand with two nucleotides bound to each subunit. However, the chemo-mechanical coupling mechanism in unwinding has yet to be elucidated. Here, we utilized nanotensioner-enhanced Förster resonance energy transfe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa057
更新日期:2020-04-06 00:00:00
abstract::Hepatitis B viruses, or hepadnaviruses, are small DNA-containing viruses that replicate through reverse transcription. Their prototype, HBV, causes severe liver disease in humans. The hepadnaviral P protein is an unusual reverse transcriptase (RT) that initiates DNA synthesis by host-factor-dependent protein priming o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.7.1679
更新日期:2002-04-01 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
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更新日期:1995-02-11 00:00:00
abstract::Melanotransferrin (MTf) is a tumor associated antigen found in abundance on the surface of melanoma cells. It is a transferrin-like protein found in low amount in most adult tissues and whose gene is reminiscent of house-keeping genes. With the goal of understanding the regulatory mechanisms which might explain the en...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.11.2853
更新日期:1992-06-11 00:00:00
abstract::The effect of different levels of mercury substitution on the rate and extent of hybridisation of globin mRNA with a complementary DNA (cDNA) copy has been investigated. It was found that mercuration significantly reduces both the rate of hybridisation and the extent of the reaction, but that these effects are abolish...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.8.2357
更新日期:1979-12-20 00:00:00
abstract::Type II restriction endonucleases Bam HI and Eco RI were covalently coupled to Sepharose. These insolubilized enzymes generated fragment patterns for several viral DNAs identical to those produced by the respective free enzymes. Conditions for optimal activity were similar for both bound and unbound forms of the enzym...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.3.679
更新日期:1978-03-01 00:00:00
abstract::Bacteria from the genus Streptomyces are very important for the production of natural bioactive compounds such as antibiotic, antitumour or immunosuppressant drugs. Around two-thirds of all known natural antibiotics are produced by these bacteria. An enormous quantity of crucial data related to this genus has been gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1253
更新日期:2013-01-01 00:00:00
abstract::Translation is a key regulatory step, linking transcriptome and proteome. Two major methods of translatome investigations are RNC-seq (sequencing of translating mRNA) and Ribo-seq (ribosome profiling). To facilitate the investigation of translation, we built a comprehensive database TranslatomeDB (http://www.translato...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1034
更新日期:2018-01-04 00:00:00
abstract::The Human Disease Ontology (DO) (http://www.disease-ontology.org), database has undergone significant expansion in the past three years. The DO disease classification includes specific formal semantic rules to express meaningful disease models and has expanded from a single asserted classification to include multiple-...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2019-01-08 00:00:00
abstract::Neph et al. (2012) (Circuitry and dynamics of human transcription factor regulatory networks. Cell, 150: 1274-1286) reported the transcription factor (TF) regulatory networks of 41 human cell types using the DNaseI footprinting technique. This provides a valuable resource for uncovering regulation principles in differ...
journal_title:Nucleic acids research
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doi:10.1093/nar/gku923
更新日期:2014-11-10 00:00:00
abstract::Plasmid encoded replication initiation (Rep) proteins recruit host helicases to plasmid replication origins. Previously, we showed that RepD recruits directionally the PcrA helicase to the pC221 oriD, remains associated with it, and increases its processivity during plasmid unwinding. Here we show that RepD forms a co...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2010-04-01 00:00:00
abstract::With the improved rapid sequencing techniques, the earlier sequence of U2 RNA of Novikoff hepatoma (Shibata et al, J. Biol. Chem. 250, 3909-3920, 1975) was reanalyzed and modified. The improved sequence of U2 RNA is 188 (or 189) nucleotides long and is in register with a characterized U2 RNA pseudogene (Denison et al,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.21.5645
更新日期:1981-11-11 00:00:00
abstract::Protein-DNA recognition is a critical component of gene regulatory processes but the underlying molecular mechanisms are not yet completely understood. Whereas the DNA binding preferences of transcription factors (TFs) are commonly described using nucleotide sequences, the 3D DNA structure is recognized by proteins an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt862
更新日期:2014-01-01 00:00:00