Abstract:
:Here, we present an update of Breast Cancer Now Tissue Bank bioinformatics, a rich platform for the sharing, mining, integration and analysis of breast cancer data. Its modalities provide researchers with access to a centralised information gateway from which they can access a network of bioinformatic resources to query findings from publicly available, in-house and experimental data generated using samples supplied from the Breast Cancer Now Tissue Bank. This in silico environment aims to help researchers use breast cancer data to their full potential, irrespective of any bioinformatics barriers. For this new release, a complete overhaul of the IT and bioinformatic infrastructure underlying the portal has been conducted and a host of novel analytical modules established. We developed and adopted an automated data selection and prioritisation system, expanded the data content and included tissue and cell line data generated from The Cancer Genome Atlas and the Cancer Cell Line Encyclopedia, designed a host of novel analytical modalities and enhanced the query building process. Furthermore, the results are presented in an interactive format, providing researchers with greater control over the information on which they want to focus. Breast Cancer Now Tissue Bank bioinformatics can be accessed at http://bioinformatics.breastcancertissuebank.org/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Gadaleta E,Pirrò S,Dayem Ullah AZ,Marzec J,Chelala Cdoi
10.1093/nar/gkx913subject
Has Abstractpub_date
2018-01-04 00:00:00pages
D1055-D1061issue
D1eissn
0305-1048issn
1362-4962pii
4372709journal_volume
46pub_type
杂志文章abstract::We report here spectroscopic and biochemical data of a novel series of sugar-modified oligodeoxy-nucleotides, the carbocyclic oligothymidylates, c(dT)3-20. In c(dT)n a methylene group has been substituted for the oxygen atom of the deoxyribose ring of the natural thymidylate unit. c(dT)10-20 form helical structures, i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.8.2133
更新日期:1990-04-25 00:00:00
abstract::The 80S ribosome from Saccharomyces cerevisiae has been reconstructed from cryo electron micrographs to a resolution of 35 A. It is strikingly similar to the 70S ribosome from Escherichia coli, while displaying the characteristic eukaryotic features familiar from reconstructions of ribosomes from higher eukaryotes. As...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.2.655
更新日期:1998-01-15 00:00:00
abstract::A growing body of evidence suggests that siRNA could generate off-target effects through different mechanisms. However, the full impact of off-target gene regulation on phenotypic induction and accordingly on data interpretation in the context of large-scale siRNA library screen has not been reported. Here we report o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki762
更新日期:2005-08-09 00:00:00
abstract::In Euplotes crassus millions of telomeres are synthesized during the sexual phase of the life cycle. Since these newly synthesized telomeres are longer than normal macronuclear telomeres, they must be trimmed to the mature size. We have examined the timing and mechanism of this trimming step. We have shown that a sudd...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.23.5366
更新日期:1993-11-25 00:00:00
abstract::Escherichia coli seryl-tRNA synthetase (SerRS) is a homo-dimeric class II aminoacyl-tRNA synthetase. Each subunit is composed of two distinct domains: the N-terminal domain is a 60 A long, arm-like coiled coil structure built up of two antiparallel alpha-helices, whereas the C-terminal domain, the catalytic core, is a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.7.1113
更新日期:1995-04-11 00:00:00
abstract::Short oligo(deoxynucleoside phosphorothioate)s were analyzed as a pool of individual diastereomeric species. The composition of such mixtures, determined by means of HPLC, indicates that consecutive couplings in commonly used phosphoramidite chemistry lead to increasing contents of the Rp isomer. Methods of analysis a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.3.530
更新日期:1995-02-11 00:00:00
abstract::The Sleeping Beauty (SB) transposon is a promising gene transfer vector that integrates nonspecifically into host cell genomes. Herein, we attempt to direct transposon integration into predetermined DNA sites by coupling a site-specific DNA-binding domain (DBD) to the SB transposase. We engineered fusion proteins comp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm089
更新日期:2007-01-01 00:00:00
abstract::We have developed a novel method of genetic library construction on magnetic microbeads based on solid-phase single-molecule PCR in a fine and robust water-phase compartment formed in water-in-oil (w/o) emulsions. In this method, critically diluted DNA fragments were distributed over the emulsion as templates, where b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gni143
更新日期:2005-10-06 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
pub_type: 杂志文章
doi:10.1093/nar/gkm203
更新日期:2007-01-01 00:00:00
abstract::Pyrimidine adducts in cellular DNA arise from modification of the pyrimidine 5,6-double bond by oxidation, reduction or hydration. The biological outcome includes increased mutation rate and potential lethality. A major DNA N:-glycosylase responsible for the excision of modified pyrimidine bases is the base excision r...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.3.604
更新日期:2001-02-01 00:00:00
abstract::Short repetitive DNA sequences are believed to be one of the primordial genetic elements that served as a source of complex large DNA found in the genome of modern organisms. However, the mechanism of its expansion (increase in repeat number) during the course of evolution is unclear. We demonstrate that the DNA polym...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.20.3999
更新日期:2000-10-15 00:00:00
abstract::DNA methylation plays a crucial role in the establishment of tissue-specific gene expression and the regulation of key biological processes. However, our present inability to predict the effect of genome sequence variation on DNA methylation precludes a comprehensive assessment of the consequences of non-coding variat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx177
更新日期:2017-06-20 00:00:00
abstract::A class II site-specific endodeoxyribonuclease (SalPI) was identified in cell-free extracts of Streptomyces albus CMI 52766 after high speed centrifugation and fractionation through Bio Gel AO.5M. SalPI cleaves lambda DNA into at least 18 fragments. Five cleavage sites were located in the linear lambda map by the use ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.6.1989
更新日期:1977-06-01 00:00:00
abstract::Oriented DNA films prepared by the wet-spinning technique have been complexed with several ligands: the anthracycline antibiotic violamycin BI, the dipeptide L-carnosine, and the oligopeptide antibiotic netropsin. The formation of the DNA-ligand complexes is accompanied by dramatic changes of the conformational flexib...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.23.9165
更新日期:1984-12-11 00:00:00
abstract::Most human genes generate multiple transcript isoforms. The differential expression of these isoforms can help specify cell types. Diverse transcript isoforms arise from the use of alternative transcription start sites, polyadenylation sites and splice sites; however, the relative contribution of these processes to is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1165
更新日期:2018-01-25 00:00:00
abstract::The pac1+ gene of the fission yeast Schizosaccharomyces pombe is essential for viability and its overexpression induces sterility and suppresses mutations in the pat1+ and snm1+ genes. The pac1+ gene encodes a protein that is structurally similar to RNase III from Escherichia coli, but its normal function is unknown. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.12.2377
更新日期:1996-06-15 00:00:00
abstract::The rpoA gene, encoding the alpha subunit of RNA polymerase, was cloned from Streptomyces coelicolor A3(2). It is preceded by rpsK and followed by rplQ, encoding ribosomal proteins S11 and L17, respectively, similar to the gene order in Bacillus subtilis. The rpoA gene specifies a protein of 339 amino acids with deduc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.22.4565
更新日期:1996-11-15 00:00:00
abstract::The purpose of the proposed web server, publicly available at http://paccmit.epfl.ch, is to provide a user-friendly interface to two algorithms for predicting messenger RNA (mRNA) molecules regulated by microRNAs: (i) PACCMIT (Prediction of ACcessible and/or Conserved MIcroRNA Targets), which identifies primarily mRNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv457
更新日期:2015-07-01 00:00:00
abstract::We have isolated a unique fragment of the HLA-DR alpha gene and probed human genomic DNA at low stringency to search for homologous sequences. A minimum of six non-polymorphic cross-hybridizing high molecular weight fragments were found in all DNAs examined. In order to obtain molecular clones of these cross-hybridizi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.20.7515
更新日期:1985-10-25 00:00:00
abstract::Cell differentiation is a central process in development and in cancer growth and dissemination. OCT4 (POU5F1) and NANOG are essential for cell stemness and pluripotency; yet, the mechanisms that regulate their expression remain largely unknown. Repetitive elements account for almost half of the Human Genome; still, t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw095
更新日期:2016-06-02 00:00:00
abstract::Amino acid sequences of 2 giant non-structural polyproteins (F1 and F2) of infectious bronchitis virus (IBV), a member of Coronaviridae, were compared, by computer-assisted methods, to sequences of a number of other positive strand RNA viral and cellular proteins. By this approach, juxtaposed putative RNA-dependent RN...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.12.4847
更新日期:1989-06-26 00:00:00
abstract::The kinetics of PaeR7 endonuclease-catalysed cleavage reactions of fluorophor-labeled oligonucleotide substrates have been examined using fluorescence resonance energy transfer (FRET). A series of duplex substrates were synthesized with an internal CTCGAG PaeR7 recognition site and donor (fluorescein) and acceptor (rh...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.15.3155
更新日期:1994-08-11 00:00:00
abstract::Small regulatory RNAs (sRNAs) from bacterial chromosomes became the focus of research over the past five years. However, relatively little is known in terms of structural requirements, kinetics of interaction with their targets and degradation in contrast to well-studied plasmid-encoded antisense RNAs. Here, we presen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm439
更新日期:2007-01-01 00:00:00
abstract::Understanding interactions between proteins and RNA is key to deciphering the mechanisms of many important biological processes. Here we describe RNABindR, a web-based server that identifies and displays RNA-binding residues in known protein-RNA complexes and predicts RNA-binding residues in proteins of unknown struct...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm294
更新日期:2007-07-01 00:00:00
abstract::The assembly of the complex that forms over the simian virus 40 origin to initiate DNA replication is not well understood. This complex is composed of the virus-coded T antigen and three cellular proteins, replication protein A (RPA), DNA polymerase alpha/primase (pol/prim) and topoisomerase I (topo I) in association ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh236
更新日期:2004-02-11 00:00:00
abstract::Two of the tRNA's found in rabbit reticulocytes are substrates for a post-transcriptional modification leading to the incorporation of guanine into the polynucleotide chain. The major guanylated tRNA was previously identified as tRNA (His). In the present report we show that the minor guanylated tRNA is tRNA (Asn), an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/3.10.2521
更新日期:1976-10-01 00:00:00
abstract::The recognition of human tRNA(Leu) or tRNA(Ser) by cognate aminoacyl- tRNA synthetases has distinct requirements. Only one base change (A73-->G) in tRNA(Leu) is required to generate an efficient serine acceptor in vitro, whereas several changes in three structural domains (the acceptor stem, DHU loop and long extra ar...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.3.405
更新日期:1996-02-01 00:00:00
abstract::The alternative proliferating-cell nuclear antigen (PCNA)-loader CTF18-RFC forms a stable complex with DNA polymerase ε (Polε). We observed that, under near-physiological conditions, CTF18-RFC alone loaded PCNA inefficiently, but loaded it efficiently when complexed with Polε. During efficient PCNA loading, CTF18-RFC ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx096
更新日期:2017-05-05 00:00:00
abstract::Cellular membranes feature dynamic submicrometer-scale lateral domains termed lipid rafts, membrane rafts or glycosphingolipid-enriched microdomains (GEM). Numerous proteomics studies have been conducted on the lipid raft proteome, however, interpretation of individual studies is limited by potential undefined contami...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky948
更新日期:2019-01-08 00:00:00
abstract::Two new endonuclease activities, endonuclease B and endonuclease C, obtained from yeast nuclear preparations have been separated and partially characterized. Endonuclease B has a primary requirement for Mn2+ which cannot be replaced by Mg2+ or Ca2+, and makes single-strand scissions in double-stranded DNA. Endonculeas...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.7.1023
更新日期:1975-07-01 00:00:00