Abstract:
:The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a premier public resource for literature-based, manually curated associations between chemicals, gene products, phenotypes, diseases, and environmental exposures. In this biennial update, we present our new chemical-phenotype module that codes chemical-induced effects on phenotypes, curated using controlled vocabularies for chemicals, phenotypes, taxa, and anatomical descriptors; this module provides unique opportunities to explore cellular and system-level phenotypes of the pre-disease state and allows users to construct predictive adverse outcome pathways (linking chemical-gene molecular initiating events with phenotypic key events, diseases, and population-level health outcomes). We also report a 46% increase in CTD manually curated content, which when integrated with other datasets yields more than 38 million toxicogenomic relationships. We describe new querying and display features for our enhanced chemical-exposure science module, providing greater scope of content and utility. As well, we discuss an updated MEDIC disease vocabulary with over 1700 new terms and accession identifiers. To accommodate these increases in data content and functionality, CTD has upgraded its computational infrastructure. These updates continue to improve CTD and help inform new testable hypotheses about the etiology and mechanisms underlying environmentally influenced diseases.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Davis AP,Grondin CJ,Johnson RJ,Sciaky D,McMorran R,Wiegers J,Wiegers TC,Mattingly CJdoi
10.1093/nar/gky868subject
Has Abstractpub_date
2019-01-08 00:00:00pages
D948-D954issue
D1eissn
0305-1048issn
1362-4962pii
5106145journal_volume
47pub_type
杂志文章abstract::The transcriptional activity of the p53 tumor suppressor protein is crucial for the regulation of cell growth, apoptosis and tumor progression. The first identified p53 relative, p73, was reported to be monoallelically expressed in normal tissues. In some tumors, loss of heterozygosity was associated with overexpressi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.2.513
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abstract::RegPredict web server is designed to provide comparative genomics tools for reconstruction and analysis of microbial regulons using comparative genomics approach. The server allows the user to rapidly generate reference sets of regulons and regulatory motif profiles in a group of prokaryotic genomes. The new concept o...
journal_title:Nucleic acids research
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doi:10.1093/nar/gkq531
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abstract::The equilibrium binding of ethidium bromide to native DNAs and to poly(dG-dC) X poly(dG-dC) has been studied by both phase partition and direct spectrophotometric techniques. The binding isotherms obtained from both experimental techniques show that ethidium binds in a cooperative manner to E. coli DNA. On the other h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.24.8211
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv959
更新日期:2015-12-15 00:00:00
abstract::In mammalian cells, DNA double-strand breaks (DSBs) are repaired by three pathways, nonhomologous end-joining (NHEJ), gene conversion (GC) and single-strand annealing (SSA). These pathways are distinct with regard to repair efficiency and mutagenic potential and must be tightly controlled to preserve viability and gen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn347
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abstract::A normal human population has been screened for the existence of further restriction fragment length polymorphisms (RFLPs) in the clotting factor IX gene in addition to the TaqI polymorphism already characterised (1,2). Two polymorphic loci were found, both within 6 Kb of the TaqI polymorphism within the body of the f...
journal_title:Nucleic acids research
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doi:10.1093/nar/12.23.8861
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abstract::To investigate the feasibility of conducting a genomic-scale protein labeling and localization study in Escherichia coli, a representative subset of 23 coding DNA sequences (CDSs) was selected for chromosomal tagging with one or more fluorescent protein genes (EGFP, EYFP, mRFP1, DsRed2). We used lambda-Red recombinati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1158
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abstract::The enzyme endonuclease V nicks uracil-containing DNA at the second or third phosphodiester bond 3' to uracil sites. I applied the enzyme to random fragmentation of DNA to revise the complex DNA shuffling protocol. The merit of using endonuclease V is that cleavage occurs at random sites and the length of the fragment...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnf139
更新日期:2002-12-15 00:00:00
abstract::Four phage clones which hybridize with U1 small nuclear RNA were obtained from a rat gene library. Two clones contain a presumed pseudogene. A third clone includes two gene candidates that are co-linear with the rat U1-RNA, 3.6kb apart and in the opposite orientation. The two genes are surrounded by identical sequence...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.6.1791
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abstract::Alpha-1-microglobulin and bikunin are two plasma glycoproteins encoded by an alpha-1-microglobulin/bikunin precursor (AMBP) gene. The strict liver-specific expression of the AMBP gene is controlled by a potent enhancer made of six clustered boxes numbered 1-6 that have been reported to be proven or potential binding s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.3.395
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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::Detection of cell-free DNA in liquid biopsies offers great potential for use in non-invasive prenatal testing and as a cancer biomarker. Fetal and tumor DNA fractions however can be extremely low in these samples and ultra-sensitive methods are required for their detection. Here, we report an extremely simple and fast...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw224
更新日期:2016-06-20 00:00:00
abstract::In this paper, we report the cloning and sequencing of the C. elegans histidyl-tRNA synthetase gene. The complete genomic sequence, and most of the cDNA sequence, of this gene is now determined. The gene size including flanking and coding regions is 2230 nucleotides long. Three small introns (45-50 bp long) are found ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.18.4344
更新日期:1993-09-11 00:00:00
abstract::Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5' Untranslated Regions (5'UTRs) and N-terminal coding sequences. Accurate transcriptome-wide detection of alternative first exons typically requires specialized experimental approaches that are designed to identify the 5' ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky053
更新日期:2018-05-04 00:00:00
abstract::Myocyte enhancer binding factor 2 (MEF2) proteins belong to the MADS box family of transcription factors and four MEF2 proteins, MEF2A, MEF2B, MEF2C and MEF2D, have been found. MEF2 proteins have been shown to play critical roles in differentiation of muscles and neuronal tissues. How transactivational activity of MEF...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.13.2836
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abstract::Previous work has demonstrated that the yeast SPT3 gene is required for transcription from delta sequences, the long terminal repeats that flank yeast Ty elements. In spt3 null mutants, transcription fails to initiate in delta sequences and instead initiates farther downstream. Null mutations in SPT3 cause other mutan...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.17.6885
更新日期:1986-09-11 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1157
更新日期:2012-04-01 00:00:00
abstract::The rol-6 gene is trans-spliced to the 22 nt leader, SL1, 173 nt downstream of the transcription start. We have analyzed splicing in transformants carrying extrachromosomal arrays of rol-6 with mutations in the trans-splice acceptor site. This site is a close match to the consensus, UUUCAG, that is highly conserved in...
journal_title:Nucleic acids research
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doi:10.1093/nar/21.4.913
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky199
更新日期:2018-04-20 00:00:00
abstract::The DNA data bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) maintains a primary nucleotide sequence database and provides analytical resources for biological information to researchers. This database content is exchanged with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics ...
journal_title:Nucleic acids research
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doi:10.1093/nar/gks1152
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abstract::In HIV-1 infection, Tat acts at least in part to control transcriptional elongation by overcoming premature transcriptional termination. In some other genes this process is governed by DNA elements called attenuators in concert with cellular transcription factors. To understand the action of Tat more fully and explore...
journal_title:Nucleic acids research
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doi:10.1093/nar/25.24.5017
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.10.3375
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journal_title:Nucleic acids research
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doi:10.1093/nar/gkq481
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journal_title:Nucleic acids research
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journal_title:Nucleic acids research
pub_type: 杂志文章
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku230
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky704
更新日期:2018-09-28 00:00:00