Abstract:
:MatrixDB (http://matrixdb.ibcp.fr) is a freely available database focused on interactions established by extracellular proteins and polysaccharides. Only few databases report protein-polysaccharide interactions and, to the best of our knowledge, there is no other database of extracellular interactions. MatrixDB takes into account the multimeric nature of several extracellular protein families for the curation of interactions, and reports interactions with individual polypeptide chains or with multimers, considered as permanent complexes, when appropriate. MatrixDB is a member of the International Molecular Exchange consortium (IMEx) and has adopted the PSI-MI standards for the curation and the exchange of interaction data. MatrixDB stores experimental data from our laboratory, data from literature curation, data imported from IMEx databases, and data from the Human Protein Reference Database. MatrixDB is focused on mammalian interactions, but aims to integrate interaction datasets of model organisms when available. MatrixDB provides direct links to databases recapitulating mutations in genes encoding extracellular proteins, to UniGene and to the Human Protein Atlas that shows expression and localization of proteins in a large variety of normal human tissues and cells. MatrixDB allows researchers to perform customized queries and to build tissue- and disease-specific interaction networks that can be visualized and analyzed with Cytoscape or Medusa.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Chautard E,Fatoux-Ardore M,Ballut L,Thierry-Mieg N,Ricard-Blum Sdoi
10.1093/nar/gkq830subject
Has Abstractpub_date
2011-01-01 00:00:00pages
D235-40issue
Database issueeissn
0305-1048issn
1362-4962pii
gkq830journal_volume
39pub_type
杂志文章abstract::We present a study of how substituent groups of naturally occurring and modified nucleotide bases affect the degree of hydration of right-handed B-DNA and left-handed Z-DNA. A comparison of poly(dG-dC) and poly(dG-dm5C) titrations with the lipotropic salts of the Hofmeister series infers that the methyl stabilization ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.25.5978
更新日期:1993-12-25 00:00:00
abstract::An improved method was developed for microdissection and cloning of metaphase as well as pachytene chromosomes. The protocol incorporates efficient ligation of chromosomal DNA with linker adaptors, abolishment of microcloning steps and the reduction of micromanipulation. The threshold for amplifying genomic DNA templa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.17.3555
更新日期:1997-09-01 00:00:00
abstract::The interaction of several synthetic analogues of d-ApA with Poly U and Poly dT was examined to explore the effects of substituents at phosphorus on binding properties of oligonucleotides. These analogues contained a bulky, lipophilic group (2,2,2-trichloroethoxy or 2,2,2-trichloro-1,1-dimethylethoxy) a small, uncharg...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.8.3487
更新日期:1986-04-25 00:00:00
abstract::DNA dodecamers have been designed with two cytosines on each end and intervening A and T stretches, such that the oligomers have fully complementary A:T base pairs when aligned in the parallel orientation. Spectroscopic (UV, CD and IR), NMR and molecular dynamics studies have shown that oligomers having the sequences ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.7.1500
更新日期:2002-04-01 00:00:00
abstract::Three different types of repetitive Eco RI fragments, which comigrate within a visible band of approximately 500 bp at gel electrophoresis of Xenopus laevis DNA Eco RI digests have been cloned and sequenced. These sequences are designated as Repetitive Eco RI Monomers: REM 1, REM 2 and REM 3. The sequences contain dir...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.12.4921
更新日期:1984-06-25 00:00:00
abstract::MicroRNA (miRNA) 5'-isoforms, or 5'-isomiRs, are small-RNA species that originate from the same genomic loci as the major miRNAs with their 5' ends shifted from the 5' ends of the miRNAs by a few nucleotides. Although 5'-isomiRs have been reported, their origins, properties and potential functions remain to be examine...
journal_title:Nucleic acids research
pub_type: 杂志文章,meta分析
doi:10.1093/nar/gkt967
更新日期:2014-02-01 00:00:00
abstract::During the past years, the advances in high-throughput technologies have produced an unprecedented growth in the number and size of repositories and databases storing relevant biological data. Today, there is more biological information than ever but, unfortunately, the current status of many of these repositories is ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks575
更新日期:2012-07-01 00:00:00
abstract::The RES complex was previously identified in yeast as a splicing factor affecting nuclear pre-mRNA retention. This complex was shown to contain three subunits, namely Snu17, Bud13 and Pml1, but its mode of action remains ill-defined. To obtain insights into its function, we have performed a structural investigation of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn894
更新日期:2009-01-01 00:00:00
abstract::The gene-external part of the human 7S L promoter was analyzed by transcription in vitro and in vivo. Compared to the wild type promoter (-178), a -66 5'deletion mutant revealed full activity in vitro but was inefficiently transcribed in vivo. Further deletion to -37 reduced template activity to 50% in vitro and to ba...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.23.6779
更新日期:1990-12-11 00:00:00
abstract::We have examined the ability of a cationic planar chromophore, ethidium bromide, to intercalate into a short, defined triple helix. Using UV absorption, fluorescence spectroscopy and a gel retardation assay we demonstrate that ethidium bromide is able to bind to a triple helix with a lower affinity than to the corresp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.7.1521
更新日期:1991-04-11 00:00:00
abstract::Multiple pathways counteract DNA replication stress to prevent genomic instability and tumorigenesis. The recently identified human SDE2 is a genome surveillance protein regulated by PCNA, a DNA clamp and processivity factor at replication forks. Here, we show that SDE2 cleavage after its ubiquitin-like domain generat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz054
更新日期:2019-05-07 00:00:00
abstract::Precursor tRNAAsp molecules, containing a 26-base 5' leader, were treated with diethylpyrocarbonate, 50% hydrazine or anhydrous hydrazine/3M NaCl and then subjected to processing by RNase P RNAs from Escherichia coli or Bacillus subtilis. Fully processed tRNAs and material not successfully cleaved by the catalytic RNA...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.4.885
更新日期:1991-02-25 00:00:00
abstract::The chemical synthesis of backbone deuterium labelled [r(CGCGAAU*U*CGCG)]2 (U* = [5'-2H]U) is described. An efficient purification procedure was developed using a polymeric reverse phase (PRP) HPLC column at 60 degrees C. This procedure provided pure RNA dodecamer in the multi-milligram quantities (39% overall yield) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.19.5131
更新日期:1992-10-11 00:00:00
abstract::Guanine rich nucleic acid sequences can form G-quadruplex (G4) structures that interfere with DNA replication, repair and RNA transcription. The human FANCJ helicase contributes to maintaining genomic integrity by promoting DNA replication through G4-forming DNA regions. Here, we combined single-molecule and ensemble ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw574
更新日期:2016-10-14 00:00:00
abstract::The CABS-fold web server provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling). The web server is based on the CABS modeling procedures ranked in previous Critical Assessment of techniques for protein Structure Prediction competi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt462
更新日期:2013-07-01 00:00:00
abstract::Targeted modulation of gene expression represents a valuable approach to understand the mechanisms governing gene regulation. In a therapeutic context, it can be exploited to selectively modify the aberrant expression of a disease-causing gene or to provide the target cells with a new function. Here, we have establish...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky171
更新日期:2018-05-18 00:00:00
abstract::We describe a novel 3'-OH unblocked reversible terminator with the potential to improve accuracy and read-lengths in next-generation sequencing (NGS) technologies. This terminator is based on 5-hydroxymethyl-2'-deoxyuridine triphosphate (HOMedUTP), a hypermodified nucleotide found naturally in the genomes of numerous ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1293
更新日期:2011-03-01 00:00:00
abstract::The proteins in a cell often assemble into complexes to carry out their functions and play an essential role of biological processes. The PCFamily server identifies template-based homologous protein complexes [called protein complex family (PCF)] and infers functional modules of the query proteins. This server first f...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq464
更新日期:2010-07-01 00:00:00
abstract::Most mutations in cancer genomes occur in the non-coding regions with unknown impact on tumor development. Although the increase in the number of cancer whole-genome sequences has revealed numerous putative non-coding cancer drivers, their information is dispersed across multiple studies making it difficult to underst...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa915
更新日期:2021-01-08 00:00:00
abstract::Alternative splicing generates multiple transcript and protein isoforms from a single gene and controls transcript intracellular localization and stability by coupling to mRNA export and nonsense-mediated mRNA decay (NMD). RNA interference (RNAi) is a potent mechanism to modulate gene expression. However, its interact...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1260
更新日期:2021-01-25 00:00:00
abstract::We have studied the regulation of DNA ligase I gene expression in UV-C irradiated human primary fibroblasts. An increase of approximately 6-fold both in DNA ligase I messenger and activity levels was observed 24 h after UV treatment, when nucleotide excision repair (NER) is no longer operating. DNA ligase I induction ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.6.962
更新日期:1995-03-25 00:00:00
abstract::Immunoglobulin genes contain a conserved eight base sequence element 5' to the site of transcription initiation. This octamer can serve as a site for the binding of nuclear proteins which are presumably involved in the cell type specific expression of this family of genes. In studying the binding of nuclear proteins t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.12.5503
更新日期:1988-06-24 00:00:00
abstract::Herein, we describe a case study into the population dynamics of in vitro selection, using RNA-cleaving DNAzymes as a model system. We sought to understand how the composition of the population can change over time in response to different levels of selection pressure, and how well these changes are correlated with se...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp222
更新日期:2009-06-01 00:00:00
abstract::Significant differences are observed between the CD spectra of eu- and heterochromatin prepared by fractionating mechanically sheared rat liver chromatin on linear sucrose density gradients. Heterochromatin has a broad positive CD at 270--280 nm, a cross-over point at 256 nmn, and a negative shoulder at 248 nm. Euchro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.4.1657
更新日期:1979-04-01 00:00:00
abstract::RNA fragments from phage fr covering the complete or part of the replicase cistron initiation region have been used as templates in the formation of a ribosomal initiation complex in vitro. The results so obtained together with our earlier findings in a similar approach applied to fragments of the structurally related...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.23.7763
更新日期:1982-12-11 00:00:00
abstract::Pathogenic bacteria encounter host-imposed manganese (Mn) limitation during infection. Herein we report that in the human pathogen Streptococcus pyogenes, the adaptive response to Mn limitation is controlled by a DtxR family metalloregulator, MtsR. Genes upregulated by MtsR during Mn limitation include Mn (mtsABC) and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz524
更新日期:2019-08-22 00:00:00
abstract::Antisense oligodeoxynucleotides targeted to Ha-ras mRNA have been designed to discriminate between the codon 12-mutated oncogene and the normal proto-oncogene. An in vitro assay using two different sources of RNase H (rabbit reticulocyte lysates and nuclear extract from HeLa cells) was used to characterize oligonucleo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.17.3411
更新日期:1995-09-11 00:00:00
abstract::Nuclear factor I (NFI) is a site-specific DNA binding protein required for the replication of adenovirus type 2 DNA in vitro and in vivo. To study sequence requirements for the interaction of NFI with DNA, we have measured the binding of the protein to a variety of synthetic sites. Binding sites for NFI (FIB sites) we...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.14.5545
更新日期:1987-07-24 00:00:00
abstract::The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS has undergone significant updates in re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1077
更新日期:2017-01-04 00:00:00
abstract::In addition to maintaining the GenBank 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 made available through NCBI's Web site. NCBI resources include Entrez, the Entrez Programming Utili...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj158
更新日期:2006-01-01 00:00:00