Abstract:
:The Diatom Expressed Sequence Tag (EST) Database was constructed to provide integral access to ESTs from these ecologically and evolutionarily interesting microalgae. It has now been updated with 130,000 Phaeodactylum tricornutum ESTs from 16 cDNA libraries and 77,000 Thalassiosira pseudonana ESTs from seven libraries, derived from cells grown in different nutrient and stress regimes. The updated relational database incorporates results from statistical analyses such as log-likelihood ratios and hierarchical clustering, which help to identify differentially expressed genes under different conditions, and allow similarities in gene expression in different libraries to be investigated in a functional context. The database also incorporates links to the recently sequenced genomes of P. tricornutum and T. pseudonana, enabling an easy cross-talk between the expression pattern of diatom orthologs and the genome browsers. These improvements will facilitate exploration of diatom responses to conditions of ecological relevance and will aid gene function identification of diatom-specific genes and in silico gene prediction in this largely unexplored class of eukaryotes. The updated Diatom EST Database is available at http://www.biologie.ens.fr/diatomics/EST3.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Maheswari U,Mock T,Armbrust EV,Bowler Cdoi
10.1093/nar/gkn905subject
Has Abstractpub_date
2009-01-01 00:00:00pages
D1001-5issue
Database issueeissn
0305-1048issn
1362-4962pii
gkn905journal_volume
37pub_type
杂志文章abstract::The gene encoding myelin basic protein (MBP) contains multiple activator sequences spanning upstream of its transcriptional initiation site which differentially promote transcription in glial cells. The proximal activator sequence, designated MB1, activates transcription in a glial cell type specific manner. This sequ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.3.545
更新日期:1992-02-11 00:00:00
abstract::An intronic hexanucleotide UGCAUG has been shown to play a critical role in the regulation of tissue-specific alternative splicing of pre-mRNAs in a wide range of tissues. Vertebrate Fox-1 has been shown to bind to this element, in a highly sequence-specific manner, through its RNA recognition motif (RRM). In mammals,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki338
更新日期:2005-04-11 00:00:00
abstract::Boundary elements partition eukaryotic chromatin into active and repressive domains, and can also block regulatory interactions between domains. Boundary elements act via diverse mechanisms making accurate feature-based computational predictions difficult. Therefore, we developed an unbiased algorithm that predicts th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr750
更新日期:2012-01-01 00:00:00
abstract::In the present study, the relationship between short interfering RNA (siRNA) sequence and RNA interference (RNAi) effect was extensively analyzed using 62 targets of four exogenous and two endogenous genes and three mammalian and Drosophila cells. We present the rules that may govern siRNA sequence preference and in a...
journal_title:Nucleic acids research
pub_type: 指南,杂志文章
doi:10.1093/nar/gkh247
更新日期:2004-02-09 00:00:00
abstract::The high-throughput sequencing of nuclease-protected mRNA fragments bound to ribosomes, a technique known as ribosome profiling, quantifies the relative frequencies with which different regions of transcripts are translated. This technique has revealed novel translation initiation sites with unprecedented scope and ha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv200
更新日期:2015-04-20 00:00:00
abstract::Genomic Denaturing Gradient Gel Electrophoresis (gDGGE) provides an alternative to the standard method of restriction fragment length polymorphism (RFLP) analysis for identifying polymorphic sequence variation in genomic DNA. For gDGGE, genomic DNA is cleaved by restriction enzymes, separated in a polyacrylamide gel c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.7.1475
更新日期:1991-04-11 00:00:00
abstract::In Saccharomyces cerevisiae, the stability of highly repetitive rDNA array is maintained through transcriptional silencing. Recently, a β-1,3-glucanosyltransferase Gas1 has been shown to play a significant role in the regulation of transcriptional silencing in S. cerevisiae. Here, we show that the gas1Δ mutation incre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku570
更新日期:2014-07-01 00:00:00
abstract::Previous evidence indicates that telomeres resemble common fragile sites and present a challenge for DNA replication. The precise impediments to replication fork progression at telomeric TTAGGG repeats are unknown, but are proposed to include G-quadruplexes (G4) on the G-rich strand. Here we examined DNA synthesis and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt813
更新日期:2013-12-01 00:00:00
abstract::Previously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints in a query sequence and assigns to each position of the sequence one of the major HIV-1 subtypes. Since incorrect subtype assignment or recombinatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp371
更新日期:2009-07-01 00:00:00
abstract::In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utiliti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm1000
更新日期:2008-01-01 00:00:00
abstract::With the increasing number of protein structures available, there is a need for tools capable of automating the comparison of ensembles of structures, a common requirement in structural biology and bioinformatics. PSSweb is a web server for protein structural statistics. It takes as input an ensemble of PDB files of p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw332
更新日期:2016-07-08 00:00:00
abstract::We describe a method for the formation of hybrid genes by in vivo recombination between two genes with partial sequence homology. DNA structures consisting of plasmid vector sequences, flanked by the alpha 2 interferon gene on the one side and a portion of the alpha 1 interferon gene (homology about 80%) on the other,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.16.5661
更新日期:1983-08-25 00:00:00
abstract::Transcription initiation complexes formed by bacterial RNA polymerases (RNAPs) exhibit dramatic species-specific differences in stability, leading to different strategies of transcription regulation. The molecular basis for this diversity is unclear. Promoter complexes formed by RNAP from Thermus aquaticus (Taq) are c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks973
更新日期:2012-12-01 00:00:00
abstract::Transposable elements are found throughout the genomes of all organisms. Repressive marks such as DNA methylation and histone H3 lysine 9 (H3K9) methylation silence these elements and maintain genome integrity. However, how silencing mechanisms are themselves regulated to avoid the silencing of genes remains unclear. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv958
更新日期:2016-01-29 00:00:00
abstract::The beta-globin gene of a patient with mRNA-deficient beta o-thalassemia has been sequenced. We find a single nucleotide deletion in amino acid codon 44 that produces a UGA terminator at codon 60. We have previously shown that the beta-globin mRNA of this patient is correctly spliced and polyadenylated, but rapidly tu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.18.5421
更新日期:1982-09-25 00:00:00
abstract::The complete nucleotide sequence of the Escherichia coli recB gene which encodes a subunit of the ATP-dependent DNase, Exonuclease V, has been determined. The proposed coding region for the RecB protein is 3543 nucleotides long and would encode a polypeptide of 1180 amino acids with a calculated molecular weight of 13...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.21.8573
更新日期:1986-11-11 00:00:00
abstract::The mission of UniProt is to support biological research by providing a freely accessible, stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with extensive cross-references and querying interfaces. UniProt is comprised of four major components, each optimized for ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr981
更新日期:2012-01-01 00:00:00
abstract::5-methylcytosine (m5C) modifications of RNA are ubiquitous in nature and play important roles in many biological processes such as protein translational regulation, RNA processing and stress response. Aberrant expressions of RNA:m5C methyltransferases are closely associated with various human diseases including cancer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx473
更新日期:2017-06-20 00:00:00
abstract::Multiple sequence alignments play a central role in the annotation of novel genomes. Given the biological and computational complexity of this task, the automatic generation of high-quality alignments remains challenging. Since multiple alignments are usually employed at the very start of data analysis pipelines, it i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki1020
更新日期:2005-12-16 00:00:00
abstract::MHCPEP is a curated database comprising over 6000 peptide sequences known to bind MHC molecules. Entries are compiled from published reports as well as from direct submissions of experimental data. Each entry contains peptide sequence, MHC specificity and when available, experimental method, observed activity, binding...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.1.242
更新日期:1996-01-01 00:00:00
abstract::p53 as an effector of nucleolar stress is well defined, but p53 independent mechanisms are largely unknown. Like p53, the NF-κB transcription factor plays a critical role in maintaining cellular homeostasis under stress. Many stresses that stimulate NF-κB also disrupt nucleoli. However, the link between nucleolar func...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky455
更新日期:2018-07-06 00:00:00
abstract::Allele-specific DNA methylation, histone acetylation and histone methylation are recognized as epigenetic characteristics of imprinted genes and imprinting centers (ICs). These epigenetic modifications are also used to regulate tissue-specific gene expression. Epigenetic differences between alleles can be significant ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh671
更新日期:2004-06-24 00:00:00
abstract::A simple, two-step method is described for the synthesis of the 5'-pyro- and triphosphate derivatives of 3'-5' ApA, ApG, GpA and GpG. The readily accessible 2'(3')-5' ApA, ApG, GpA and GpG were converted in one step to the corresponding 5'-phosphoramidate derivatives which were then transformed to the 5'-pyro- and tri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.8.2945
更新日期:1978-08-01 00:00:00
abstract::The human gene for plasminogen activator inhibitor type-1 (PAI-1) has been isolated and its promoter region characterized. PAI-1 regulation by glucocorticoids, transforming growth factor-beta (TGF-beta) and the phorbol ester PMA is shown to be exerted at the promoter level. A fragment spanning 805 nucleotides of the 5...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.7.2805
更新日期:1988-04-11 00:00:00
abstract::The spliceosomal protein Prp1 (Prp6/U5-102 K) is necessary for the integrity of pre-catalytic spliceosomal complexes. We have identified a novel regulatory function for Prp1. Expression of mutations in the N-terminus of Prp1 leads to the accumulation of pre-catalytic spliceosomal complexes containing the five snRNAs U...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1155
更新日期:2010-03-01 00:00:00
abstract::We have characterized elongation complexes (ECs) of RNA polymerase from the extremely thermophilic bacterium, Thermus thermophilus. We found that complexes assembled on nucleic acid scaffolds are transcriptionally competent at high temperature (50-80 degrees C) and, depending upon the organization of the scaffold, pos...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl559
更新日期:2006-01-01 00:00:00
abstract::The RosettaDesign server identifies low energy amino acid sequences for target protein structures (http://rosettadesign.med.unc.edu). The client provides the backbone coordinates of the target structure and specifies which residues to design. The server returns to the client the sequences, coordinates and energies of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl163
更新日期:2006-07-01 00:00:00
abstract::A method is presented for the purification of mRNAs and the identification of structural gene sequences in recombinant DNA molecules. RNA is hybridized to double-stranded linear DNA such that R-loops are formed between most DNAs and their complementary RNA sequences. These R-loops are purified from unhybridized RNAs b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.7.2483
更新日期:1979-06-11 00:00:00
abstract::PAX6 is a transcription factor that plays a major role in ocular morphogenesis. PAX6 is expressed in the eye, central nervous system and pancreas. Two alternative promoters, P0 and P1, which are differentially regulated during development, drive PAX6 transcription. We identified a 57 bp cis-regulatory element in exon ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.19.4070
更新日期:2001-10-01 00:00:00
abstract::Mismatch uracil DNA glycosylase (Mug) from Escherichia coli is an initiating enzyme in the base-excision repair pathway. As with other DNA glycosylases, the abasic product is potentially more harmful than the initial lesion. Since Mug is known to bind its product tightly, inhibiting enzyme turnover, understanding how ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq913
更新日期:2011-04-01 00:00:00