Abstract:
:Reactome (http://www.reactome.org) is a manually curated open-source open-data resource of human pathways and reactions. The current version 46 describes 7088 human proteins (34% of the predicted human proteome), participating in 6744 reactions based on data extracted from 15 107 research publications with PubMed links. The Reactome Web site and analysis tool set have been completely redesigned to increase speed, flexibility and user friendliness. The data model has been extended to support annotation of disease processes due to infectious agents and to mutation.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Croft D,Mundo AF,Haw R,Milacic M,Weiser J,Wu G,Caudy M,Garapati P,Gillespie M,Kamdar MR,Jassal B,Jupe S,Matthews L,May B,Palatnik S,Rothfels K,Shamovsky V,Song H,Williams M,Birney E,Hermjakob H,Stein L,D'Eustadoi
10.1093/nar/gkt1102subject
Has Abstractpub_date
2014-01-01 00:00:00pages
D472-7issue
Database issueeissn
0305-1048issn
1362-4962pii
gkt1102journal_volume
42pub_type
杂志文章abstract::Eucaryotic ribosome biogenesis involves many cis-acting sequences and trans-acting factors, including snoRNAS: We have used directed mutagenesis of rDNA plasmids in yeast to identify critical sequence and structural elements within and flanking the ITS2-proximal stem. This base paired structure, present in the mature ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.10.2106
更新日期:2001-05-15 00:00:00
abstract::Plasmodium falciparum origin recognition complex 1 (ORC1) protein has been implicated in DNA replication and silencing var gene family. However, the mechanism and the domain structure of ORC1 related to the regulation of var gene family are unknown. Here we show that the unique N-terminus of PfORC1 (PfORC1N(1-238)) is...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks202
更新日期:2012-07-01 00:00:00
abstract::We have microinjected genomic DNA clones containing the Moloney murine leukemia virus (M-MuLV) proviral genome and flanking mouse sequences from Mov-3, Mov-7 and Mov-10 mice into Xenopus laevis oocytes and analyzed the virus-specific transcription and translation products. These mouse strains carry a proviral genome c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.12.3989
更新日期:1983-06-25 00:00:00
abstract::We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki232
更新日期:2005-02-08 00:00:00
abstract::The abundance of Alu RNA is transiently increased by heat shock in human cell lines. This effect is specific to Alu repeats among Pol III transcribed genes, since the abundance of 7SL, 7SK, 5S and U6 RNAs is essentially unaffected by heat shock. The rapid induction of Alu expression precedes the heat shock induction o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.10.1758
更新日期:1995-05-25 00:00:00
abstract::Transcription of RNA from the beta-globin (major) gene in nuclei from induced mouse erythroleukemia cells terminates within the region between 700 to 2000 bases downstream from the poly(A) addition site, but not at particularly favored sites. In addition we present the first analysis of in vivo labeled RNA from a cell...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.22.8723
更新日期:1984-11-26 00:00:00
abstract::Human transcription factor Sp1 contains three contiguous repeats of the C2H2-type zinc finger motif and binds to the decanucleotide sequence 5'-(G/T)GGGCGG(G/A)(G/A)(C/T)-3' (GC box). In order to determine whether the three-zinc finger peptide Sp1(530-623) has selectivity for sequence outside the GC box, we used a sel...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.24.4920
更新日期:2001-12-15 00:00:00
abstract::The RNA degradosome is a multi-enzyme assembly that contributes to key processes of RNA metabolism, and it engages numerous partners in serving its varied functional roles. Small domains within the assembly recognize collectively a diverse range of macromolecules, including the core protein components, the cytoplasmic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks739
更新日期:2012-11-01 00:00:00
abstract::We investigated the effects of the antiviral agent distamycin A and of a distamycin derivative (FCE 24517) which possesses antineoplastic activity on the binding of some regulatory proteins to DNA. Both compounds inhibited the binding to DNA of the ubiquitous octamer binding factor OTF 1 and of the erythroid specific ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.3.1051
更新日期:1989-02-11 00:00:00
abstract::Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw162
更新日期:2016-04-20 00:00:00
abstract:UNLABELLED:Synonymous codon usage biases are associated with various biological factors, such as gene expression level, gene length, gene translation initiation signal, protein amino acid composition, protein structure, tRNA abundance, mutation frequency and patterns, and GC compositions. Quantification of codon usage ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm392
更新日期:2007-07-01 00:00:00
abstract::The Saccharomyces cerevisiae kinase/adenosine triphosphatase Rio1 regulates rDNA transcription and segregation, pre-rRNA processing and small ribosomal subunit maturation. Other roles are unknown. When overexpressed, human ortholog RIOK1 drives tumor growth and metastasis. Likewise, RIOK1 promotes 40S ribosomal subuni...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky618
更新日期:2018-09-06 00:00:00
abstract::It has been shown that the monomethylated cap structure plays important roles in pre-mRNA splicing and nuclear export of RNA. As a candidate for the factor involved in these nuclear events we have previously purified an 80 kDa nuclear cap binding protein (NCBP) from a HeLa cell nuclear extract and isolated its full-le...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.18.3638
更新日期:1995-09-25 00:00:00
abstract::The role of the mRNA-binding protein human antigen R (HuR) in stabilization and translation of AU-rich elements (ARE) containing mRNAs is well established. However, the trafficking of HuR and bound mRNA cargo, which comprises a fundamental requirement for the aforementioned HuR functions is only poorly understood. By ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt663
更新日期:2013-10-01 00:00:00
abstract::Daunomycin is one of the most important agents used in anticancer chemotherapy. It interacts with DNA through intercalation of its planar chromophore between successive base pairs. The effect of intercalation on structure, dynamics and energetics is the topic of a wealth of scientific studies. In the present study, we...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh788
更新日期:2004-09-01 00:00:00
abstract::Fundamental aspects of the biochemistry of Type III restriction endonucleases remain unresolved despite being characterized by numerous research groups in the past decades. One such feature is the subunit stoichiometry of these hetero-oligomeric enzyme complexes, which has important implications for the reaction mecha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku122
更新日期:2014-04-01 00:00:00
abstract::Here we compare several methods for predicting oligonucleotide frequencies in 691 kb of Drosophila melanogaster DNA. As in previous work on Escherichia coli and Saccharomyces cerevisiae, a relatively simple equation based on tetranucleotide frequencies can be used in predicting frequencies of higher order oligonucleot...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.14.3651
更新日期:1992-07-25 00:00:00
abstract::Here we report proof-of-principle for a microsphere-based genotyping assay that detects single nucleotide polymorphisms (SNPs) directly from human genomic DNA samples. This assay is based on a structure-specific cleavage reaction that achieves single base discrimination with a 5'-nuclease which recognizes a tripartite...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng066
更新日期:2003-06-01 00:00:00
abstract::The regions of the polypeptide chain immediately preceding or following an α-helix are known as Nt- and Ct cappings, respectively. Cappings play a central role stabilizing α-helices due to lack of intrahelical hydrogen bonds in the first and last turn. Sequence patterns of amino acid type preferences have been derived...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr879
更新日期:2012-01-01 00:00:00
abstract::Deamination of cytosine (C), 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC) occurs spontaneously in mammalian DNA with several hundred deaminations occurring in each cell every day. The resulting potentially mutagenic mispairs of uracil (U), thymine (T) or 5-hydroxymethyluracil (hmU) with guanine (G) are subs...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks259
更新日期:2012-07-01 00:00:00
abstract::A set of programs is presented for the reconstruction of a DNA sequence from data generated by the M13 shotgun sequencing technique. Once the sequence has been established and stored other programs are used for its analysis. The programs have been written for the Apple II microcomputer. A minimum investment is require...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.1.39
更新日期:1982-01-11 00:00:00
abstract::We describe mGene.web, a web service for the genome-wide prediction of protein coding genes from eukaryotic DNA sequences. It offers pre-trained models for the recognition of gene structures including untranslated regions in an increasing number of organisms. With mGene.web, users have the additional possibility to tr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp479
更新日期:2009-07-01 00:00:00
abstract::Histone H3K4 methylation is an epigenetic mark associated with actively transcribed genes. This modification is catalyzed by the mixed lineage leukaemia (MLL) family of histone methyltransferases including MLL1, MLL2, MLL3, MLL4, SET1A and SET1B. The catalytic activity of this family is dependent on interactions with ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz697
更新日期:2019-09-26 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::In eukaryotes, the tRNA-mimicking polypeptide-chain release factor, eRF1, decodes stop codons on the ribosome in a complex with eRF3; this complex exhibits striking structural similarity to the tRNA-eEF1A-GTP complex. Although amino acid residues or motifs of eRF1 that are critical for stop codon discrimination have b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv376
更新日期:2015-05-19 00:00:00
abstract::Studies of bacterial chromosomes and plasmids indicate that their replication initiator proteins bind to origins of replication at many double-stranded sites and also at AT-rich regions where single-stranded DNA is exposed during origin opening. Single-strand binding apparently promotes origin opening by stabilizing a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa826
更新日期:2020-11-04 00:00:00
abstract::JSNP is a repository of Japanese Single Nucleotide Polymorphism (SNP) data, begun in 2000 and developed through the Prime Minister's Millennium Project. The aim of this undertaking is to identify and collate up to 150 000 SNPs from the Japanese population, located in genes or in adjacent regions that might influence t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.1.158
更新日期:2002-01-01 00:00:00
abstract::We have cloned and mapped the sequences extending 38 kb 3' of the c-myc gene. This region is found to be highly repetitive in nature and hybridizes extensively with a BLUR 8 Alu probe. Unique sequence probes derived from this region were used to map the chromosomal breakpoints of a number of lymphoma cell lines with t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.10.4037
更新日期:1986-05-27 00:00:00
abstract::Deregulation of mini-chromosome maintenance (MCM) proteins is associated with genomic instability and cancer. MCM complexes are recruited to replication origins for genome duplication. Paradoxically, MCM proteins are in excess than the number of origins and are associated with chromatin regions away from the origins d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt022
更新日期:2013-03-01 00:00:00
abstract::Myotonic dystrophy type 1 (DM1) is caused by the expansion of a (CTG).(CAG) repeat in the DMPK gene on chromosome 19q13.3. At least 17 neurological diseases have similar genetic mutations, the expansion of DNA repeats. In most of these disorders, the disease severity is related to the length of the repeat expansion, a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh976
更新日期:2004-12-01 00:00:00