Abstract:
:The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) provides information about interactions between environmental chemicals and gene products and their relationships to diseases. Chemical-gene, chemical-disease and gene-disease interactions manually curated from the literature are integrated to generate expanded networks and predict many novel associations between different data types. CTD now contains over 15 million toxicogenomic relationships. To navigate this sea of data, we added several new features, including DiseaseComps (which finds comparable diseases that share toxicogenomic profiles), statistical scoring for inferred gene-disease and pathway-chemical relationships, filtering options for several tools to refine user analysis and our new Gene Set Enricher (which provides biological annotations that are enriched for gene sets). To improve data visualization, we added a Cytoscape Web view to our ChemComps feature, included color-coded interactions and created a 'slim list' for our MEDIC disease vocabulary (allowing diseases to be grouped for meta-analysis, visualization and better data management). CTD continues to promote interoperability with external databases by providing content and cross-links to their sites. Together, this wealth of expanded chemical-gene-disease data, combined with novel ways to analyze and view content, continues to help users generate testable hypotheses about the molecular mechanisms of environmental diseases.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Davis AP,Murphy CG,Johnson R,Lay JM,Lennon-Hopkins K,Saraceni-Richards C,Sciaky D,King BL,Rosenstein MC,Wiegers TC,Mattingly CJdoi
10.1093/nar/gks994subject
Has Abstractpub_date
2013-01-01 00:00:00pages
D1104-14issue
Database issueeissn
0305-1048issn
1362-4962pii
gks994journal_volume
41pub_type
杂志文章abstract::A dnaB-like protein from P. aeruginosa was purified to near homogeneity using as an assay the immunoprecipitation by E. coli dnaB antiserum in a solid-phase. In the chromatographic characteristics including the affinity to immobilized ATP the dnaB-like protein of P. aeruginosa is similar to the dnaB protein of E. coli...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.2.385
更新日期:1987-01-26 00:00:00
abstract::Most proteins from higher organisms are known to be multi-domain proteins and contain substantial numbers of intrinsically disordered (ID) regions. To analyse such protein sequences, those from human for instance, we developed a special protein-structure-prediction pipeline and accumulated the products in the Structur...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1057
更新日期:2011-01-01 00:00:00
abstract::Base specificity in the interaction of ethidium with double stranded synthetic RNA homopolymers has been studied by means of spectroscopic (UV-visible absorption and fluorescence), microcalorimetric and dilatometric techniques. The results show a strong base specificity in this interaction, the association constant wi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.14.5803
更新日期:1987-07-24 00:00:00
abstract::We have previously shown that in vivo estradiol-dependent dephosphorylation of MDBP-2-H1 (a member of the histone H1 family) correlates with the loss of in vitro preferential binding to methylated DNA. To study the effects of the phosphorylation/dephosphorylation of MDBP-2-H1 on the expression of the avian vitellogeni...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.10.1816
更新日期:1996-05-15 00:00:00
abstract::An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA pr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx598
更新日期:2017-09-19 00:00:00
abstract::The isolation and characterization of deletion mutants of the bacteriocinogenic plasmid Clo DF13 is described. To construct these deletion mutants, DNA of Clo DF13::Tn901 and Clo DF13-rep3::Tn901 plasmids was digested with restriction endonucleases, ligated with T4 ligase and introduced by transformation into Escheric...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.6.1801
更新日期:1978-06-01 00:00:00
abstract::In the most extensive examination to date of the relationship between the pausing of reverse transcrip-tase (RT) and RNA secondary structures, pause events were found to be correlated to inverted repeats both ahead of, and behind the catalytic site in vitro. In addition pausing events were strongly associated with pol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.14.3433
更新日期:1998-07-15 00:00:00
abstract::MicroRNAs (miRNAs) are small noncoding RNAs that regulate gene expression post-transcriptionally. Previous studies, which characterized miRNA function, revealed their involvement in fundamental biological processes. Importantly, miRNA expression is deregulated in many human diseases. Specific inhibition of miRNAs usin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt823
更新日期:2013-12-01 00:00:00
abstract::The genome of the cell is often exposed to DNA damaging agents and therefore requires an intricate well-regulated DNA damage response (DDR) to overcome its deleterious effects. The DDR needs proper regulation for its timely activation, repression, as well as appropriate choice of repair pathway. Studies in Saccharomyc...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkw1369
更新日期:2017-03-17 00:00:00
abstract::Transposition of Saccharomyces cerevisiae Ty1 retroelements has been shown to involve reverse transcription in intracytoplasmic virus-like particles (Ty-VLPs). Ty DNA present in the particles specified by Ty1-H3 element was found to consist of the full-length genomic DNA as well as incomplete cDNAs mainly of plus pola...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.15.3513
更新日期:1993-07-25 00:00:00
abstract::The binding kinetics of NF-kappaB p50 to the Ig-kappaB site and to a DNA duplex with no specific binding site were determined under varying conditions of potassium chloride concentration using a surface plasmonresonance biosensor. Association and dissociation rate constants were measured enabling calculation of the di...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.4.1063
更新日期:1999-02-15 00:00:00
abstract::Potential promoters in the genome of Escherichia coli were searched by pattern recognition software PlatProm and classified on the basis of positions relative to gene borders. Beside the expected promoters located in front of the coding sequences we found a considerable amount of intragenic promoter-like signals with ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp490
更新日期:2009-08-01 00:00:00
abstract::The interaction of RNase T1 with calf thymus DNA was studied using uv difference spectroscopy and the effect of the enzyme on DNA melting. There was no indication of RNase T1 binding with native DNA. A prominent difference spectrum for RNase T1 binding with denatured DNA (d-DNA) was observed at pH 5, 25 degrees and lo...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.1.11
更新日期:1975-01-01 00:00:00
abstract::We show that in mouse myoblasts the MyoD1 promoter is highly stimulated by MyoD1 expression, suggesting that it is controlled by a positive feedback loop. Using deletion and mutation analyses, we identified the targets for MyoD1 promoter autoregulation as the two proximal E-boxes located close to the MyoD1 core promot...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.12.2234
更新日期:1994-06-25 00:00:00
abstract::We have previously identified a T lymphocyte protein which binds to a site within the LTR of the human immunodeficiency virus type 1 (HIV-1) and exerts an inhibitory effect on virus gene expression. The palindromic site (site B) recognized by this protein is related to the palindromic binding sites of members of the s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.20.5429
更新日期:1992-10-25 00:00:00
abstract::RNA polymerase II (pol II) utilizes a complex interaction network to select and incorporate correct nucleoside triphosphate (NTP) substrates with high efficiency and fidelity. Our previous 'synthetic nucleic acid substitution' strategy has been successfully applied in dissecting the function of nucleic acid moieties i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw220
更新日期:2016-05-05 00:00:00
abstract::PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for biological activity data of small molecules and RNAi reagents. The mission of PubChem is to deliver free and easy access to all deposited data, and to provide intuitive data analysis tools. The PubChem BioAssay database currently contains 500,000 des...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1132
更新日期:2012-01-01 00:00:00
abstract::The human 5S rRNA genes are found in clusters of tandem repeated units. We have cloned and partially characterized six restriction fragments from two clusters of 2.3 kb and 1.6 kb repeats, respectively. Four fragments from the cluster of 2.3 kb repeats contain a 5S rRNA gene and one fragment contains a gene variant wi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.15.4147
更新日期:1991-08-11 00:00:00
abstract::Pentatricopeptide repeat (PPR) proteins are helical-repeat proteins that offer a promising scaffold for the engineering of proteins to bind specified RNAs. PPR tracts bind RNA in a modular 1-repeat, 1-nucleotide fashion. An amino acid code specifying the bound nucleotide has been elucidated. However, this code does no...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1288
更新日期:2018-03-16 00:00:00
abstract::The interaction of N--Acetyl--Phe--tRNA Phe with 70 S ribosomes is a reversible process in the absence as well as in the presence of messenger. The equilibrium binding constants of these interactions were measured at different magnesium concentrations and temperatures and thermodynamical quantities computed. The entha...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.10.3871
更新日期:1978-10-01 00:00:00
abstract::The RNA 3D Structure-to-Multiple Sequence Alignment Server (R3D-2-MSA) is a new web service that seamlessly links RNA three-dimensional (3D) structures to high-quality RNA multiple sequence alignments (MSAs) from diverse biological sources. In this first release, R3D-2-MSA provides manual and programmatic access to cu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv543
更新日期:2015-07-01 00:00:00
abstract::The CDC16 gene is involved in the process of chromosome segregation in mitosis and a cdc16ts mutant accumulates the predominant microtubule-associated protein at the nonpermissive temperature. We find that the CDC16 gene open reading frame (ORF) is capable of encoding a protein whose calculated molecular weight and pI...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.20.8439
更新日期:1987-10-26 00:00:00
abstract::Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolution of 3.2 Å. This structure shows the stalk region and the essentia...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1165
更新日期:2017-01-25 00:00:00
abstract::Here we describe a method of labelling short oligonucleotide probes with enzyme without purification or chemical modifications. Biotinylated oligonucleotides as short as 10 nt are coupled with streptavidin-conjugated enzyme, hybridised and detected with enzyme-triggered chemiluminescence. The detection of hybridisatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.2.703
更新日期:1999-01-15 00:00:00
abstract::Virtually the whole region of the mobile dispersed genetic element mdg1 including the direct repeats that frame mdg1 /1/ is transcribed. The end of the transcriptional unit is located within the direct repeat. Although the transcription of mdg1 is symmetric, one direction is transcribed preferentially and is a full-le...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.22.5347
更新日期:1980-11-25 00:00:00
abstract::Active DNA demethylation is crucial for epigenetic control, but the underlying enzymatic mechanisms are incompletely understood. REPRESSOR OF SILENCING 1 (ROS1) is a 5-methylcytosine (5-meC) DNA glycosylase/lyase that initiates DNA demethylation in plants through a base excision repair process. The enzyme binds DNA no...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt625
更新日期:2013-10-01 00:00:00
abstract::Giant viruses have extraordinarily large dsDNA genomes, and exceptionally, they encode various components of the translation apparatus, including tRNAs, aminoacyl-tRNA synthetases and translation factors. Here, we focused on the elongation factor 1 (EF1) family of viral translational GTPases (trGTPases), using computa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz296
更新日期:2019-06-20 00:00:00
abstract::Previously, we have shown that all class-1 polypeptide release factors (RFs) share a common glycine-glycine-glutamine (GGQ) motif, which is critical for RF activity. Here, we subjected to site-directed mutagenesis two invariant amino acids, Gln185 and Arg189, situated in the GGQ minidomain of human eRF1, followed by d...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.19.3982
更新日期:2001-10-01 00:00:00
abstract::The recent outbreak of COVID-19 has generated an enormous amount of Big Data. To date, the COVID-19 Open Research Dataset (CORD-19), lists ∼130,000 articles from the WHO COVID-19 database, PubMed Central, medRxiv, and bioRxiv, as collected by Semantic Scholar. According to LitCovid (11 August 2020), ∼40,300 COVID19-re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa969
更新日期:2021-01-08 00:00:00
abstract::Oriented DNA films prepared by the wet-spinning technique have been complexed with several ligands: the anthracycline antibiotic violamycin BI, the dipeptide L-carnosine, and the oligopeptide antibiotic netropsin. The formation of the DNA-ligand complexes is accompanied by dramatic changes of the conformational flexib...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.23.9165
更新日期:1984-12-11 00:00:00