Abstract:
:IMP (Integrative Multi-species Prediction), originally released in 2012, is an interactive web server that enables molecular biologists to interpret experimental results and to generate hypotheses in the context of a large cross-organism compendium of functional predictions and networks. The system provides biologists with a framework to analyze their candidate gene sets in the context of functional networks, expanding or refining their sets using functional relationships predicted from integrated high-throughput data. IMP 2.0 integrates updated prior knowledge and data collections from the last three years in the seven supported organisms (Homo sapiens, Mus musculus, Rattus norvegicus, Drosophila melanogaster, Danio rerio, Caenorhabditis elegans, and Saccharomyces cerevisiae) and extends function prediction coverage to include human disease. IMP identifies homologs with conserved functional roles for disease knowledge transfer, allowing biologists to analyze disease contexts and predictions across all organisms. Additionally, IMP 2.0 implements a new flexible platform for experts to generate custom hypotheses about biological processes or diseases, making sophisticated data-driven methods easily accessible to researchers. IMP does not require any registration or installation and is freely available for use at http://imp.princeton.edu.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wong AK,Krishnan A,Yao V,Tadych A,Troyanskaya OGdoi
10.1093/nar/gkv486subject
Has Abstractpub_date
2015-07-01 00:00:00pages
W128-33issue
W1eissn
0305-1048issn
1362-4962pii
gkv486journal_volume
43pub_type
杂志文章abstract::A major goal of system biology is the characterization of transcription factors and microRNAs (miRNAs) and the transcriptional programs they regulate. We present Allegro, a method for de-novo discovery of cis-regulatory transcriptional programs through joint analysis of genome-wide expression data and promoter or 3' U...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn1064
更新日期:2009-04-01 00:00:00
abstract::CTCF plays a pivotal role in mediating chromatin interactions, but it does not do so alone. A number of factors have been reported to co-localize with CTCF and regulate CTCF loops, but no comprehensive analysis of binding partners has been performed. This prompted us to identify CTCF loop participants and regulators b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa705
更新日期:2020-09-25 00:00:00
abstract::Spirochetes of the genus Borrelia include the tick-transmitted causative agents of Lyme disease and relapsing fever. They possess unusual genomes composed mainly of linear replicons terminated by closed DNA hairpin telomeres. Hairpin telomeres present an uninterrupted DNA chain to the replication machinery overcoming ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt832
更新日期:2013-12-01 00:00:00
abstract::MAGIA(2) (http://gencomp.bio.unipd.it/magia2) is an update, extension and evolution of the MAGIA web tool. It is dedicated to the integrated analysis of in silico target prediction, microRNA (miRNA) and gene expression data for the reconstruction of post-transcriptional regulatory networks. miRNAs are fundamental post...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks460
更新日期:2012-07-01 00:00:00
abstract::We have used in vitro transcription in isolated pea nuclei to determine whether the expression of genes for the seed storage proteins legumin and vicilin is regulated transcriptionally or post-transcriptionally in response to changing sulfur status in the developing seed. During the first 48 h of recovery from S defic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/13.3.999
更新日期:1985-02-11 00:00:00
abstract::During protein synthesis, the nascent peptide chain traverses the peptide exit tunnel of the ribosome. We monitor the co-translational movement of the nascent peptide using a fluorescent probe attached to the N-terminus of the nascent chain. Due to fluorophore quenching, the time-dependent fluorescence signal emitted ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky740
更新日期:2018-12-14 00:00:00
abstract::The functionalisation of oligodeoxynucleotides and oligoribonucleotides by incorporation of 2'-amido-2'-deoxyribonucleosides, possibly containing a reporter group via the 2'-amido bond, was examined. Therefore 2'-acetamido-ribonucleosides containing a small methyl group at the 2'-amido bond were synthesized as model c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.1.51
更新日期:1995-01-11 00:00:00
abstract::The major mRNA degradation pathway involves deadenylation of the target molecule followed by decapping and, finally, 5'-->3' exonuclease digestion of the mRNA body. While yeast factors involved in the decapping and exonuclease degradation steps have been identified, the nature of the factor(s) involved in the deadenyl...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.12.2448
更新日期:2001-06-15 00:00:00
abstract::The IMGT/HLA database (http://www.ebi.ac.uk/imgt/hla) has provided a centralized repository for the sequences of the alleles named by the WHO Nomenclature Committee for Factors of the HLA System for the past four years. Since its initial release the database has grown and is the primary source of information for the s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg070
更新日期:2003-01-01 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::The 34-nucleotide trans-activator (TA) located within the RNA-2 of Red clover necrotic mosaic virus folds into a simple hairpin. The eight-nucleotide TA loop base pairs with eight complementary nucleotides in the TA binding sequence (TABS) of the capsid protein subgenomic promoter on RNA-1 and trans-activates subgenom...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh585
更新日期:2004-05-20 00:00:00
abstract::Primer design is a fundamental technique that is widely used for polymerase chain reaction (PCR). Although many methods have been proposed for primer design, they require a great deal of manual effort to generate feasible and valid primers, including homology tests on off-target sequences using BLAST-like tools. That ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv632
更新日期:2015-11-16 00:00:00
abstract::Transcription factor binding sites (TFBSs) are short DNA sequences interacting with transcription factors (TFs), which regulate gene expression. Due to the relatively short length of such binding sites, it is largely unclear how the specificity of protein-DNA interaction is achieved. Here, we have performed a genome-w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl248
更新日期:2006-05-02 00:00:00
abstract::Post-transcriptional modifications are characteristic features of tRNAs and have been shown in a number of cases to influence both their structural and functional properties, including structure stabilization, amino-acylation and codon recognition. We have developed an approach which allows the investigation of the po...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.3.756
更新日期:1999-02-01 00:00:00
abstract::Reverse transcription of HIV-1 RNA is initiated from the 3' end of a tRNA3Lys molecule annealed to the primer binding site (PBS). An additional interaction between the anticodon loop of tRNA3Lys and a viral A-rich loop is required for efficient initiation of reverse transcription of the HIV-1 MAL isolate. In the HIV-1...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg754
更新日期:2003-10-01 00:00:00
abstract::Few transcriptional regulatory networks have been described in non-model organisms. In Entamoeba histolytica seminal aspects of pathogenesis are transcriptionally controlled, however, little is known about transcriptional regulatory networks that effect gene expression in this parasite. We used expression data from tw...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm028
更新日期:2007-01-01 00:00:00
abstract::A new procedure for the purification of B. subtilis RNA polymerase, based on mild lysis of cells, low speed centrifugation, gel filtration, DEAE-Sephadex chromatography and affinity chromatography on DNA-cellulose, yields three forms of enzyme referred here as enzyme A, B and C. As revealed by SDS gel electrophoresis,...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.3.603
更新日期:1977-03-01 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::Several proteins that have substantially diverged during evolution retain similar three-dimensional structures and biological function inspite of poor sequence identity. The database on Genomic Distribution of protein structural domain Superfamilies (GenDiS) provides record for the distribution of 4001 protein domains...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki087
更新日期:2005-01-01 00:00:00
abstract::We have developed a new bioinformatics approach called ECMFinder (Evolutionary Conserved Motif Finder). This program searches for a given DNA motif within the entire genome of one species and uses the gene association information of a potential transcription factor-binding site (TFBS) to screen the homologous regions ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp077
更新日期:2009-04-01 00:00:00
abstract::The rRNA WWW Server at URL http://rrna.uia.ac.be/ now provides a database of 496 large subunit ribosomal RNA sequences. All these sequences are aligned, incorporate secondary structure information, and can be obtained in a number of formats. Other information about the sequences, such as literature references, accessi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.1.183
更新日期:1998-01-01 00:00:00
abstract::The excision of specific DNA sequences from integrated transgenes in insects permits the dissection in situ of structural elements that may be important in controlling gene expression. Furthermore, manipulation of potential control elements in the context of a single integration site mitigates against insertion site i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng148
更新日期:2003-11-15 00:00:00
abstract::A non-enzymic protein factor that increases the in vitro rate of synthesis by HeLa DNA polymerase alpha 15- to 30-fold with denatured DNA as template has been partially purified from the cytoplasmic fraction of HeLa cells. The stimulatory effect is highly specific for HeLa DNA polymerase alpha and for DNA templates th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.1.221
更新日期:1978-01-01 00:00:00
abstract::X-linked agammaglobulinemia (XLA) is an immunodeficiency caused by mutations in the gene coding for Bruton's agammaglobulinemia tyrosine kinase (BTK). A database (BTKbase) of BTK mutations has been compiled and the recent update lists 368 entries from 318 unrelated families showing 228 unique molecular events. In addi...
journal_title:Nucleic acids research
pub_type: 杂志文章,多中心研究
doi:10.1093/nar/25.1.166
更新日期:1997-01-01 00:00:00
abstract::A general approach for the synthesis of oligonucleotide-triplet phosphoramidites and the synthesis of four such blocks are described. A strategy was devised to minimize the number of dimer precursors needed for synthesis of a complete set of triplet-amidite blocks encoding all 20 amino acids. Whereas synthesis of 20 t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.22.4677
更新日期:1995-11-25 00:00:00
abstract::G-quadruplexes play various roles in multiple biological processes, which can be positive when a G4 is involved in the regulation of gene expression or detrimental when the folding of a stable G4 impairs DNA replication promoting genome instability. This duality interrogates the significance of their presence within g...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz463
更新日期:2019-07-09 00:00:00
abstract::TORQUE is a tool for cross-species querying of protein-protein interaction networks. It aims to answer the following question: given a set of proteins constituting a known complex or a pathway in one species, can a similar complex or pathway be found in the protein network of another species? To this end, Torque seeks...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp474
更新日期:2009-07-01 00:00:00
abstract::We describe a new, broadly applicable methodology for screening in parallel interactions of RNA-binding proteins (RBPs) with large numbers of microRNA (miRNA) precursors and for determining their affinities in native form in the presence of cellular factors. The assays aim at identifying pre-miRNAs that are potentiall...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1197
更新日期:2013-02-01 00:00:00
abstract::Peptidases, their substrates and inhibitors are of great relevance to biology, medicine and biotechnology. The MEROPS database (http://merops.sanger.ac.uk) aims to fulfil the need for an integrated source of information about these. The database has hierarchical classifications in which homologous sets of peptidases a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr987
更新日期:2012-01-01 00:00:00
abstract::Current literature describes several methods for the design of efficient siRNAs with 19 perfectly matched base pairs and 2 nt overhangs. Using four independent databases totaling 3336 experimentally verified siRNAs, we compared how well several of these methods predict siRNA cleavage efficiency. According to receiver ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm088
更新日期:2007-01-01 00:00:00