Abstract:
:The EcoCyc database describes the genome and gene products of Escherichia coli, its metabolic and signal-transduction pathways, and its tRNAs. The database describes 4391 genes of E.coli, 695 enzymes encoded by a subset of these genes, 904 metabolic reactions that occur in E.coli, and the organization of these reactions into 129 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc has many references to the primary literature, and is a (qualitative) computational model of E. coli metabolism. EcoCyc is available at URL http://ecocyc. PangeaSystems.com/ecocyc/
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Karp PD,Riley M,Paley SM,Pellegrini-Toole A,Krummenacker Mdoi
10.1093/nar/27.1.55subject
Has Abstractpub_date
1999-01-01 00:00:00pages
55-8issue
1eissn
0305-1048issn
1362-4962pii
gkc052journal_volume
27pub_type
杂志文章abstract::Proteomic and RNomic approaches have identified many components of different ribonucleoprotein particles (RNPs), yet still little is known about the organization and protein proximities within these heterogeneous and highly dynamic complexes. Here we describe a targeted cross-linking approach, which combines cross-lin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1366
更新日期:2016-02-18 00:00:00
abstract::A short histone-like fusion RNA, generated when the RNA 3' processing signal from a mouse histone H4 gene is inserted into a heterologous transcription unit, becomes correctly down-regulated in G1-arrested cells of a temperature-sensitive mouse mastocytoma cell cycle mutant (21-Tb; Stauber et al., EMBO J. 5, 3297-3303...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.20.9399
更新日期:1988-10-25 00:00:00
abstract::We examined the influence of the tetratricopeptide repeat factor XAB2 on chromosomal break repair, and found that XAB2 promotes end resection that generates the 3' ssDNA intermediate for homologous recombination (HR). Namely, XAB2 is important for chromosomal double-strand break (DSB) repair via two pathways of HR tha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw275
更新日期:2016-07-08 00:00:00
abstract::The sequence requirements for transcriptional stimulation of the adenovirus major late promoter (MLP) by the products of the early transcription unit Ela and by the replication of viral DNA were analyzed by in vitro transcription. Sequences upstream of +33 are involved in the moderate Ela-responsiveness of the MLP, wh...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.9.3771
更新日期:1988-05-11 00:00:00
abstract::The transcription of ribosomal genes in a cell line (Kc) derived from female D.melanogaster, has been investigated using hybridization probes prepared from restriction fragments of a cloned rDNA repeat with a 5 kb type I [Wellauer et al. (1978) Cell 14, 269-278] intron. Gels, of nuclear RNA that have been transferred ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.1.67
更新日期:1980-01-11 00:00:00
abstract::Posttranslational modifications (PTMs) of histones represent a crucial regulatory mechanism of nucleosome and chromatin dynamics in various of DNA-based cellular processes, such as replication, transcription and DNA damage repair. Lysine succinylation (Ksucc) is a newly identified histone PTM, but its regulation and f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa663
更新日期:2020-09-25 00:00:00
abstract::We have developed an information repository named SpliceInfo to collect the occurrences of the four major alternative-splicing (AS) modes in human genome; these include exon skipping, 5'-alternative splicing, 3'-alternative splicing and intron retention. The dataset is derived by comparing the nucleotide and protein s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki129
更新日期:2005-01-01 00:00:00
abstract::Four hundred twenty-eight high-resolution DNA-protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π-contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteri...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku269
更新日期:2014-06-01 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::Mouse embryo fibroblasts (MEFs) are convenient sources for biochemical studies when cell number in mouse embryos is limiting. To derive the imprinting signature of MEFs and potentially detect novel imprinted genes we performed strand- and allele-specific RNA deep sequencing. We used sequenom allelotyping in embryo and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1042
更新日期:2014-02-01 00:00:00
abstract::Minichromosome maintenance (MCM) proteins facilitate replication by licensing origins and unwinding the DNA double strand. Interestingly, the number of MCM hexamers greatly exceeds the number of firing origins suggesting additional roles of MCMs. Here we show a hitherto unanticipated function of MCM2 in cilia formatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky945
更新日期:2019-01-10 00:00:00
abstract::We have studied the ability of the wt1 tumor suppressor gene product to repress different classes of activation domains previously shown to stimulate the initiation and elongation steps of RNA polymerase II transcription in vivo. Repression assays revealed that WT1 represses all three classes of activation domains: Sp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.14.2889
更新日期:1999-07-15 00:00:00
abstract::During translation initiation, eukaryotic initiation factor 2 (eIF2) delivers the Met-tRNA to the 40S ribosomal subunit to locate the initiation codon (AUGi) of mRNA during the scanning process. Stress-induced eIF2 phosphorylation leads to a general blockade of translation initiation and represents a key antiviral pat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw172
更新日期:2016-05-19 00:00:00
abstract::Protein-RNA interactions in small nuclear ribonucleoproteins (UsnRNPs) from HeLa cells were investigated by irradiation of purified nucleoplasmic snRNPs U1 to U6 with UV light at 254 nm. The cross-linked proteins were analyzed on one- and two-dimensional gel electrophoresis systems, and the existence of a stable cross...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.23.10985
更新日期:1988-12-09 00:00:00
abstract::A library of three synthetic ribozymes with randomized arms, targeting NUX, GUX and NXG triplets, respectively, were used to identify ribozyme-accessible sites on the HIV-1 LTR transcript comprising positions -533 to 386. Three cleavable sites were identified at positions 109, 115 and 161. Ribozymes were designed agai...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.21.4059
更新日期:2000-11-01 00:00:00
abstract::We have previously reported the human cDNA encoding MSSP-1, a sequence-specific double- and single-stranded DNA binding protein [Negishi, Nishita, Saëgusa, Kakizaki, Galli, Kihara, Tamai, Miyajima, Iguchi-Ariga and Ariga (1994) Oncogene, 9, 1133-1143]. MSSP-1 binds to a DNA replication origin/transcriptional enhancer ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.25.5576
更新日期:1994-12-25 00:00:00
abstract::Preparation of large amount of single-stranded circular DNA in high selectivity is crucial for further developments of nanotechnology and other DNA sciences. Herein, a simple but practically useful methodology to prepare DNA rings has been presented. One of the essential factors is to use highly diluted T4 ligase buff...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx553
更新日期:2017-09-06 00:00:00
abstract::GGRNA (http://GGRNA.dbcls.jp/) is a Google-like, ultrafast search engine for genes and transcripts. The web server accepts arbitrary words and phrases, such as gene names, IDs, gene descriptions, annotations of gene and even nucleotide/amino acid sequences through one simple search box, and quickly returns relevant Re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks448
更新日期:2012-07-01 00:00:00
abstract::RNA-Seq is gradually becoming the standard tool for transcriptomic expression studies in biological research. Although considerable progress has been recorded in the development of statistical algorithms for the detection of differentially expressed genes using RNA-Seq data, the list of detected genes can differ signi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1273
更新日期:2015-02-27 00:00:00
abstract::The thumb subdomain, located in various family B DNA polymerases in the C-terminal region, has been shown in their crystal structures to move upon binding of DNA, changing its conformation to nearly completely wrap around the DNA. It has therefore been involved in DNA binding. In agreement with this, partial proteolys...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh184
更新日期:2004-01-16 00:00:00
abstract::The synthesis of 1-(beta-D-2'-deoxyribosyl)-2-pyrimidinone (dK) and its 5-methyl derivative (d5) from 2'-deoxycytidine or 2'-deoxythymidine, respectively, via silver oxide oxidation of 4-hydrazinopyrimidines is described. The necessary hydrazine substituted pyrimidine nucleosides have been prepared by transamination o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.6.2261
更新日期:1989-03-25 00:00:00
abstract::A role for BRCA1 in the direct and indirect regulation of transcription is well established. However, a comprehensive view of the degree to which BRCA1 impacts transcriptional regulation on a genome-wide level has not been defined. We performed genome-wide expression profiling and ChIP-chip analysis, comparison of whi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr679
更新日期:2011-12-01 00:00:00
abstract::We report a novel system for efficient and specific targeted delivery of large nucleic acids to and into cells. Plasmid DNA and core histones were assembled to chromatin by salt gradient dialysis and subsequently connected to bispecific antibody derivatives (bsAbs) via a nucleic acid binding peptide bridge. The result...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz137
更新日期:2019-06-04 00:00:00
abstract::Bacteria belonging to the class Mollicutes were among the first ones to be selected for complete genome sequencing because of the minimal size of their genomes and their pathogenicity for humans and a broad range of animals and plants. At this time six genome sequences have been publicly released (Mycoplasma genitaliu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh114
更新日期:2004-01-01 00:00:00
abstract::An 11 S ribonucleoprotein particle was isolated from maize endosperm and shown to be functionally and structurally equivalent to the mammalian signal recognition particle. However, unlike animal cells which apparently contain a single 7 SL RNA species, maize endosperm contains a heterogeneous population of 7 SL RNA. T...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.4.1573
更新日期:1989-02-25 00:00:00
abstract::We have recently developed a novel method for the affinity purification of the complete suite of translating mRNA from genetically labeled cell populations. This method permits comprehensive quantitative comparisons of the genes employed by each specific cell type. We provide a detailed description of tools for analys...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq130
更新日期:2010-07-01 00:00:00
abstract::A large number of signalling pathways converge on p53 to induce different cellular stress responses that aim to promote cell cycle arrest and repair or, if the damage is too severe, to induce irreversible senescence or apoptosis. The differentiation of p53 activity towards specific cellular outcomes is tightly regulat...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkz124
更新日期:2019-04-23 00:00:00
abstract::MicroRNAs (miRNAs) can group together along the human genome to form stable secondary structures made of several hairpins hosting miRNAs in their stems. The few known examples of such structures are all involved in cancer development. A large scale computational analysis of human chromosomes crossing sequence analysis...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt112
更新日期:2013-04-01 00:00:00
abstract::We used 2D protein gel electrophoresis and DNA microarray technologies to systematically analyze genes under glucose repression in B:acillus subtilis. In particular, we focused on genes expressed after the shift from glycolytic to gluconeogenic at the middle logarithmic phase of growth in a nutrient sporulation medium...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.3.683
更新日期:2001-02-01 00:00:00
abstract::Full-length cDNA of the 6.3 kb turnip yellow mosaic virus (TYMV) genome was placed between a T7 promoter and a unique Hind III site. In vitro transcription of Hind III-linearized DNA of clone pTYMC yielded full-length RNA transcripts. In inoculations of Chinese cabbage protoplasts and plants, capped transcripts and vi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.12.4675
更新日期:1989-06-26 00:00:00