MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks.

Abstract:

:MetaNetX is a repository of genome-scale metabolic networks (GSMNs) and biochemical pathways from a number of major resources imported into a common namespace of chemical compounds, reactions, cellular compartments--namely MNXref--and proteins. The MetaNetX.org website (http://www.metanetx.org/) provides access to these integrated data as well as a variety of tools that allow users to import their own GSMNs, map them to the MNXref reconciliation, and manipulate, compare, analyze, simulate (using flux balance analysis) and export the resulting GSMNs. MNXref and MetaNetX are regularly updated and freely available.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Moretti S,Martin O,Van Du Tran T,Bridge A,Morgat A,Pagni M

doi

10.1093/nar/gkv1117

subject

Has Abstract

pub_date

2016-01-04 00:00:00

pages

D523-6

issue

D1

eissn

0305-1048

issn

1362-4962

pii

gkv1117

journal_volume

44

pub_type

杂志文章
  • GalaxyHomomer: a web server for protein homo-oligomer structure prediction from a monomer sequence or structure.

    abstract::Homo-oligomerization of proteins is abundant in nature, and is often intimately related with the physiological functions of proteins, such as in metabolism, signal transduction or immunity. Information on the homo-oligomer structure is therefore important to obtain a molecular-level understanding of protein functions ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx246

    authors: Baek M,Park T,Heo L,Park C,Seok C

    更新日期:2017-07-03 00:00:00

  • Solid phase synthesis of the 5'-half of the initiator t-RNA from B. subtilis.

    abstract::Using cyanoethyldiisopropylamino phosphoramidite chemistry, four oligonucleotides constituting a part of the sequence of the initiator t-RNA from B. subtilis were synthesized. For the protection of the exocyclic amino functions of bases, phenoxyacetyl group was used for adenine and guanine, and acetyl group was prefer...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/17.18.7381

    authors: Chaix C,Duplaa AM,Molko D,Téoule R

    更新日期:1989-09-25 00:00:00

  • Structural organization of mRNA complexes with major core mRNP protein YB-1.

    abstract::YB-1 is a universal major protein of cytoplasmic mRNPs, a member of the family of multifunctional cold shock domain proteins (CSD proteins). Depending on its amount on mRNA, YB-1 stimulates or inhibits mRNA translation. In this study, we have analyzed complexes formed in vitro at various YB-1 to mRNA ratios, including...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh889

    authors: Skabkin MA,Kiselyova OI,Chernov KG,Sorokin AV,Dubrovin EV,Yaminsky IV,Vasiliev VD,Ovchinnikov LP

    更新日期:2004-10-19 00:00:00

  • Comparative analysis of chimeric ZFP-, TALE- and Cas9-piggyBac transposases for integration into a single locus in human cells.

    abstract::Integrating DNA delivery systems hold promise for many applications including treatment of diseases; however, targeted integration is needed for improved safety. The piggyBac (PB) transposon system is a highly active non-viral gene delivery system capable of integrating defined DNA segments into host chromosomes witho...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx572

    authors: Luo W,Galvan DL,Woodard LE,Dorset D,Levy S,Wilson MH

    更新日期:2017-08-21 00:00:00

  • Quantification of siRNA using competitive qPCR.

    abstract::We have developed a PCR-based short interfering RNA (siRNA) quantification method based on competition between siRNA and a homologous DNA primer for annealing to template DNA, avoiding the requirement for prior conversion of RNA to cDNA. Primers and probe were designed to amplify regions of the human papillomavirus E6...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkn903

    authors: Liu WL,Stevenson M,Seymour LW,Fisher KD

    更新日期:2009-01-01 00:00:00

  • The UAS of the yeast PGK gene is composed of multiple functional elements.

    abstract::The UAS (upstream activator sequence) of the yeast PGK gene contains a transcriptional activator domain located between bases -479 and -402 upstream from the initiating ATG. This region of the UAS contains three direct repeats of the sequence 5'CTTCC3'. The roles in transcriptional activation of these repeats and othe...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/16.17.8245

    authors: Chambers A,Stanway C,Kingsman AJ,Kingsman SM

    更新日期:1988-09-12 00:00:00

  • PPT-DB: the protein property prediction and testing database.

    abstract::The protein property prediction and testing database (PPT-DB) is a database housing nearly 30 carefully curated databases, each of which contains commonly predicted protein property information. These properties include both structural (i.e. secondary structure, contact order, disulfide pairing) and dynamic (i.e. orde...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkm800

    authors: Wishart DS,Arndt D,Berjanskii M,Guo AC,Shi Y,Shrivastava S,Zhou J,Zhou Y,Lin G

    更新日期:2008-01-01 00:00:00

  • Protein synthesis in rabbit reticulocytes: characteristics of CO-eIF-2 protein complex.

    abstract::A high molecular weight reticulocyte protein factor, named Co-eIF-2, contains Co-eIF-2A, Co-eIF-2B, and Co-eIF-2C activities and stimulates Met-tRNAf binding to eIF-2 both in the presence and absence of Mg2+. Some characteristics of this stimulation in the absence of Mg2+ are: (1) Stimulation is most pronounced at low...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/10.20.6501

    authors: Bagchi MK,Banerjee AC,Roy R,Chakrabarty I,Gupta NK

    更新日期:1982-10-25 00:00:00

  • Upstream box/TATA box order is the major determinant of the direction of transcription.

    abstract::Mammalian gene promoters for transcription by RNA polymerase II are typically organized in the following order: upstream sequence motif(s)/TATA box/initiation site. Here we report studies in which the order, orientation and DNA sequences of these three elements are varied to determine how these affect polarity of tran...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/19.24.6699

    authors: Xu LC,Thali M,Schaffner W

    更新日期:1991-12-25 00:00:00

  • Type III restriction endonuclease EcoP15I is a heterotrimeric complex containing one Res subunit with several DNA-binding regions and ATPase activity.

    abstract::For efficient DNA cleavage, the Type III restriction endonuclease EcoP15I communicates with two inversely oriented recognition sites in an ATP-dependent process. EcoP15I consists of methylation (Mod) and restriction (Res) subunits forming a multifunctional enzyme complex able to methylate or to cleave DNA. In this stu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkr1239

    authors: Wyszomirski KH,Curth U,Alves J,Mackeldanz P,Möncke-Buchner E,Schutkowski M,Krüger DH,Reuter M

    更新日期:2012-04-01 00:00:00

  • Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson-Crick base pairs.

    abstract::A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized in the space group I4(1)22 with the unit-cell dimensions a = b = 53.4 A and c = 54.0 A, and the crystal structure has been determined at 2.5 A resolution. The four nucleotide residues CGAA of the first half o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkf639

    authors: Sunami T,Kondo J,Kobuna T,Hirao I,Watanabe K,Miura K,Takénaka A

    更新日期:2002-12-01 00:00:00

  • The essential transcription factor Reb1p interacts with the CLB2 UAS outside of the G2/M control region.

    abstract::Regulation of CLB2 is important both for completion of the normal vegetative cell cycle in Saccharomyces cerevisiae and for departure from the vegetative cell cycle upon nitrogen deprivation. Cell cycle-regulated transcription of CLB2 in the G2/M phase is known to be brought about by a set of proteins including Mcm1p,...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg638

    authors: Van Slyke C,Grayhack EJ

    更新日期:2003-08-01 00:00:00

  • Thiostrepton-resistant mutants of Thermus thermophilus.

    abstract::Ribosomal protein L11 and its associated binding site on 23S rRNA together comprise one of the principle components that mediate interactions of translation factors with the ribosome. This site is also the target of the antibiotic thiostrepton, which has been proposed to act by preventing important structural transiti...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkh644

    authors: Cameron DM,Thompson J,Gregory ST,March PE,Dahlberg AE

    更新日期:2004-06-15 00:00:00

  • Sequences of three promoters for the bacteriophage SP6 RNA polymerase.

    abstract::Fragments of SP6 DNA generated by cleavage with Hpa II or Taq I were cloned into the Cla I site of pBR322 and the recombinant plasmids were screened for the presence of SP6 promoter activity by transcription in vitro with purified SP6 RNA polymerase. Three plasmids having promoter activity and small inserts of SP6 DNA...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.8.3521

    authors: Brown JE,Klement JF,McAllister WT

    更新日期:1986-04-25 00:00:00

  • Mammalian polyadenylation sites: implications for differential display.

    abstract::Differential display relies on a series of anchored primers to divide the total mRNA population into subsets of roughly equal size. However, this will only occur if the dinucleotide targeted by the anchor region of the anchored primers has a random frequency distribution [i.e. each of the 12 possible dinucleotides pre...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.5.1386

    authors: Frost MR,Guggenheim JA

    更新日期:1999-03-01 00:00:00

  • jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1.

    abstract::Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for subtyping and localization of phylogenetic breakpoints in HIV-1. Our software is based on a jumping profile Hidden Markov Model...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkl255

    authors: Zhang M,Schultz AK,Calef C,Kuiken C,Leitner T,Korber B,Morgenstern B,Stanke M

    更新日期:2006-07-01 00:00:00

  • The production of hybrid Ty:IFN virus-like particles in yeast.

    abstract::The yeast retrotransposon Ty encodes proteins that assemble into virus-like particles (Ty-VLPs) which can be readily purified. We have recently shown that expression of the pl protein encoded by the TYA gene of Ty is sufficient for particle formation. In this paper we show that when a heterologous coding sequence, hum...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/15.18.7571

    authors: Malim MH,Adams SE,Gull K,Kingsman AJ,Kingsman SM

    更新日期:1987-09-25 00:00:00

  • Target sites for the transposition of rat long interspersed repeated DNA elements (LINEs) are not random.

    abstract::The long interspersed repeated DNA family of rats (LINE or L1Rn family) contains about 40,000 6.7-kilobase (kb) long members (1). LINE members may be currently mobile since their presence or absence causes allelic variation at three single copy loci (2, 3): insulin 1, Moloney leukemia virus integration 2 (Mlvi-2) (4),...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/14.9.3717

    authors: Furano AV,Somerville CC,Tsichlis PN,D'Ambrosio E

    更新日期:1986-05-12 00:00:00

  • A survey of localized sequence rearrangements in human DNA.

    abstract::Genomes mutate and evolve in ways simple (substitution or deletion of bases) and complex (e.g. chromosome shattering). We do not fully understand what types of complex mutation occur, and we cannot routinely characterize arbitrarily-complex mutations in a high-throughput, genome-wide manner. Long-read DNA sequencing m...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkx1266

    authors: Frith MC,Khan S

    更新日期:2018-02-28 00:00:00

  • PARN deadenylase is involved in miRNA-dependent degradation of TP53 mRNA in mammalian cells.

    abstract::mRNA deadenylation is under the control of cis-acting regulatory elements, which include AU-rich elements (AREs) and microRNA (miRNA) targeting sites, within the 3' untranslated region (3' UTRs) of eukaryotic mRNAs. Deadenylases promote miRNA-induced mRNA decay through their interaction with miRNA-induced silencing co...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkv959

    authors: Zhang X,Devany E,Murphy MR,Glazman G,Persaud M,Kleiman FE

    更新日期:2015-12-15 00:00:00

  • Evidence that a consensus element found in naturally intronless mRNAs promotes mRNA export.

    abstract::We previously showed that mRNAs synthesized from three genes that naturally lack introns contain a portion of their coding sequence, known as a cytoplasmic accumulation region (CAR), which is essential for stable accumulation of the intronless mRNAs in the cytoplasm. The CAR in each mRNA is unexpectedly large, ranging...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gks1314

    authors: Lei H,Zhai B,Yin S,Gygi S,Reed R

    更新日期:2013-02-01 00:00:00

  • Transcription reinitiation rate: a potential role for TATA box stabilization of the TFIID:TFIIA:DNA complex.

    abstract::Potential pathways that could account for observed rapid rates of transcription reinitiation were explored. A nuclear extract system was established in which reinitiation rates were observed to be kinetically facilitated and in which the rate was sensitive to TATA box mutation. Kinetic facilitation of functional compl...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/27.3.831

    authors: Yean D,Gralla JD

    更新日期:1999-02-01 00:00:00

  • Role of RNA structure in non-homologous recombination between genomic molecules of brome mosaic virus.

    abstract::Brome mosaic virus (BMV) is a tripartite genome, positive-sense RNA virus of plants. Previously it was demonstrated that local hybridization between BMV RNAs (RNA-RNA heteroduplex formation) efficiently promotes non-homologous RNA recombination. In addition, studies on the role of the BMV polymerase in RNA recombinati...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/28.8.1714

    authors: Figlerowicz M

    更新日期:2000-04-15 00:00:00

  • Intrinsic differences between authentic and cryptic 5' splice sites.

    abstract::Cryptic splice sites are used only when use of a natural splice site is disrupted by mutation. To determine the features that distinguish authentic from cryptic 5' splice sites (5'ss), we systematically analyzed a set of 76 cryptic 5'ss derived from 46 human genes. These cryptic 5'ss have a similar frequency distribut...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkg830

    authors: Roca X,Sachidanandam R,Krainer AR

    更新日期:2003-11-01 00:00:00

  • The PKR-binding domain of adenovirus VA RNAI exists as a mixture of two functionally non-equivalent structures.

    abstract::VA RNA(I) is a non-coding adenoviral transcript that counteracts the host cell anti-viral defenses such as immune responses mediated via PKR. We investigated potential alternate secondary structure conformations within the PKR-binding domain of VA RNA(I) using site-directed mutagenesis, RNA UV-melting analysis and enz...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp595

    authors: Wahid AM,Coventry VK,Conn GL

    更新日期:2009-09-01 00:00:00

  • The mouse and human homologs of DMC1, the yeast meiosis-specific homologous recombination gene, have a common unique form of exon-skipped transcript in meiosis.

    abstract::Genetic recombination in meiosis plays an important role in generating diversity of genetic information. In yeast an Escherichia coli RecA-like gene, DMC1, is expressed in meiotic prophase and its product co-localizes with Rad51 protein on zygotene chromosomes. We have cloned the mouse and human homologs of the yeast ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/24.3.470

    authors: Habu T,Taki T,West A,Nishimune Y,Morita T

    更新日期:1996-02-01 00:00:00

  • Phospho.ELM: a database of phosphorylation sites--update 2011.

    abstract::The Phospho.ELM resource (http://phospho.elm.eu.org) is a relational database designed to store in vivo and in vitro phosphorylation data extracted from the scientific literature and phosphoproteomic analyses. The resource has been actively developed for more than 7 years and currently comprises 42,574 serine, threoni...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkq1104

    authors: Dinkel H,Chica C,Via A,Gould CM,Jensen LJ,Gibson TJ,Diella F

    更新日期:2011-01-01 00:00:00

  • Structural basis for the recognition of diastereomeric 5',8-cyclo-2'-deoxypurine lesions by the human nucleotide excision repair system.

    abstract::The hydroxyl radical is a powerful oxidant that generates DNA lesions including the stereoisomeric R and S 5',8-cyclo-2'-deoxyadenosine (cdA) and 5',8-cyclo-2'-deoxyguanosine (cdG) pairs that have been detected in cellular DNA. Unlike some other oxidatively generated DNA lesions, cdG and cdA are repaired by the human ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gku162

    authors: Kropachev K,Ding S,Terzidis MA,Masi A,Liu Z,Cai Y,Kolbanovskiy M,Chatgilialoglu C,Broyde S,Geacintov NE,Shafirovich V

    更新日期:2014-04-01 00:00:00

  • Engineering Nt.BtsCI and Nb.BtsCI nicking enzymes and applications in generating long overhangs.

    abstract::Type IIS restriction endonuclease BtsCI (GGATG 2/0) is a neoschizomer of FokI (GGATG 9/13) and cleaves closer to the recognition sequence. Although M.BtsCI shows 62% amino acid sequence identity to M.FokI, BtsCI and FokI restriction endonucleases do not share significant amino acid sequence similarity. BtsCI belongs t...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkp1092

    authors: Too PH,Zhu Z,Chan SH,Xu SY

    更新日期:2010-03-01 00:00:00

  • Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation.

    abstract::It is well established that gene regulation can be achieved through activator and repressor proteins that bind to DNA and switch particular genes on or off, and that complex metabolic networks determine the levels of transcription of a given gene at a given time. Using three complementary computational techniques to s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章

    doi:10.1093/nar/gkw815

    authors: Sutthibutpong T,Matek C,Benham C,Slade GG,Noy A,Laughton C,K Doye JP,Louis AA,Harris SA

    更新日期:2016-11-02 00:00:00