Abstract:
:With the rapid accumulation of our knowledge on diseases, disease-related genes and drug targets, network-based analysis plays an increasingly important role in systems biology, systems pharmacology and translational science. The new release of VisANT aims to provide new functions to facilitate the convenient network analysis of diseases, therapies, genes and drugs. With improved understanding of the mechanisms of complex diseases and drug actions through network analysis, novel drug methods (e.g., drug repositioning, multi-target drug and combination therapy) can be designed. More specifically, the new update includes (i) integrated search and navigation of disease and drug hierarchies; (ii) integrated disease-gene, therapy-drug and drug-target association to aid the network construction and filtering; (iii) annotation of genes/drugs using disease/therapy information; (iv) prediction of associated diseases/therapies for a given set of genes/drugs using enrichment analysis; (v) network transformation to support construction of versatile network of drugs, genes, diseases and therapies; (vi) enhanced user interface using docking windows to allow easy customization of node and edge properties with build-in legend node to distinguish different node type. VisANT is freely available at: http://visant.bu.edu.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Hu Z,Chang YC,Wang Y,Huang CL,Liu Y,Tian F,Granger B,Delisi Cdoi
10.1093/nar/gkt401subject
Has Abstractpub_date
2013-07-01 00:00:00pages
W225-31issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkt401journal_volume
41pub_type
杂志文章abstract::Influenza A virus segment 2 mRNA expresses three polypeptides: PB1, PB1-F2 and PB1-N40, from AUGs 1, 4 and 5 respectively. Two short open reading frames (sORFs) initiated by AUGs 2 and 3 are also present. To understand translational regulation in this system, we systematically mutated AUGs 1-4 and monitored polypeptid...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr487
更新日期:2011-09-01 00:00:00
abstract::Since July 1995, the European Bioinformatics Institute (EBI) has maintained RHdb (http://www.ebi.ac.uk/RHdb/RHdb.html ), a public database for radiation hybrid data. Radiation hybrid mapping is an important technique for determining high resolution maps. Recently, CORBA access has been added to Rhdb. The EBI is an Out...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.1.102
更新日期:1998-01-01 00:00:00
abstract::Unmodified tRNA molecules are useful for many purposes in cell-free protein biosynthesis, but there is little information about how the lack of tRNA post-transcriptional modifications affects the coding specificity for synonymous codons. In the present study, we prepared an unmodified form of Escherichia coli tRNA1Ser...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.15.2894
更新日期:1996-08-01 00:00:00
abstract::The -175 T greater than C mutation in the promoter of the A gamma- or G gamma-globin gene causes a 50-100 fold increase of the expression of the respective gene in adult erythroid cells (Hereditary Persistence of Fetal Hemoglobin). We show here that this mutation increases 3-9 fold the expression of a gamma-CAT report...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.14.5509
更新日期:1989-07-25 00:00:00
abstract::A lac promotor mutant was constructed by filling in the protruding ends of the HpaII site located within the lac promotor. The mutation, named M42, is a two base pair insertion that changes the distance between the -10 and -35 regions from 18 to 20 residues. The activity of the mutant promotor measured in vivo is 15% ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.3.903
更新日期:1982-02-11 00:00:00
abstract::The stable intermediates formed in the reaction of cytosine, cytidine and adenosine with chloracetaldehyde were isolated. The -CH2CH/OH/- bridge between the exo and endo nitrogen atoms of the parent base was found in these compounds by means of PMR spectroscopy. Their acid-induced dehydration resulted in formation of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.3.789
更新日期:1978-03-01 00:00:00
abstract::The nucleotide sequence of Drosophila melanogaster methionine tRNAi was determined to be: pA-G-C-A-G-A-G-U-m1G-m2G-C-G-C-A-G-U-G-G-A-A-G-C-G-U-m2G-C-U-G-G-G-C-C-C-A-U-t6A-A-C-C-C-A-G-A-G-m7G-D-m5C-C-C-G-A-G-G-A-U-C-G-m1A-A-A-C-C-U-U-G-C-U-C-U-G-C-U-A-C-C-A(OH). It differs from vertebrate initiator tRNAs in only 6 out ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/6.2.421
更新日期:1979-02-01 00:00:00
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
更新日期:2006-07-01 00:00:00
abstract::The GeneNet system is designed for collection and analysis of the data on gene and metabolic networks, signal transduction pathways and kinetic characteristics of elementary processes. In the past 2 years, the GeneNet structure was considerably improved: (i) the current version of the database is now implemented using...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki077
更新日期:2005-01-01 00:00:00
abstract::The COXPRESdb (http://coxpresdb.jp) provides gene coexpression relationships for animal species. Here, we report the updates of the database, mainly focusing on the following two points. For the first point, we added RNAseq-based gene coexpression data for three species (human, mouse and fly), and largely increased th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1163
更新日期:2015-01-01 00:00:00
abstract::DNA repair is required to maintain genome stability in stem cells and early embryos. At critical junctures, oxidative damage to DNA requires the base excision repair (BER) pathway. Since early zebrafish embryos lack the major polymerase in BER, DNA polymerase ß, repair proceeds via replicative polymerases, even though...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1142
更新日期:2011-04-01 00:00:00
abstract::FRS1 and FRS2, the structural genes encoding the large (alpha) and small (beta) subunits of yeast phenylalanyl-tRNA synthetase (PheRS) were placed under the control of the lacZ promoter by creating an artificial operon. The FRS2 gene was fused next to the promoter, followed by a 14 base pair intergenic sequence contai...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.8.2087
更新日期:1990-04-25 00:00:00
abstract::The higher order structure of the functionally important 530 loop in Escherichia coli 16S rRNA was studied in mutants with single base changes at position 517, which significantly impair translational fidelity. The 530 loop has been proposed to interact with the EF-Tu-GTP-aatRNA ternary complex during decoding. The re...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.17.3563
更新日期:1995-09-11 00:00:00
abstract::Fourteen P-element insertion mutants at the yellow (y) gene of D. melanogaster have been analysed by restriction mapping and DNA sequencing. The distribution of the insertion sites is nonrandom, with a preferred target site in the 5'-transcribed but non-translated leader of the gene. Transcription analysis indicates t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.7.3039
更新日期:1988-04-11 00:00:00
abstract::The catalytic function of the hairpin ribozyme has been investigated by modification-interference analysis of both ribozyme and substrate, using ribonucleoside phosphorothioates. Thiophosphate substitutions in two ribozyme domains were examined by using a novel and highly efficient two-piece ribozyme assembled from tw...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.11.2835
更新日期:1992-06-11 00:00:00
abstract::Although many tools have been developed to analyze small RNA sequencing (sRNA-Seq) data, it remains challenging to accurately analyze the small RNA population, mainly due to multiple sequence ID assignment caused by short read length. Additional issues in small RNA analysis include low consistency of microRNA (miRNA) ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx999
更新日期:2017-12-01 00:00:00
abstract::The synthesis of cyclic di-, tri-, tetra-, penta- and hexa-thymidylic acids (16; n = 2, 3, 4, 5 and 6) and the cyclic hexadeoxyribonucleotide [d(CpCpTpApGpGp)], via the "filtration" approach, is reported. Some of the physical properties of the cyclic oligonucleotides are discussed, and their susceptibility to digestio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.20.8221
更新日期:1989-10-25 00:00:00
abstract::Cloned DNA from the EcoRI J fragment of EBV has been used as template for in vitro transcription experiments using cell-free extracts prepared from HeLa or KB cells. Two EBV specific RNAs each about 175 bases in length were synthesised and nuclease 51 mapping experiments determined that these in vitro products corresp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.11.3407
更新日期:1982-06-11 00:00:00
abstract::Clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated Cas proteins comprise a prokaryotic RNA-guided adaptive immune system that interferes with mobile genetic elements, such as plasmids and phages. The type I-E CRISPR interference complex Cascade from Escherichia coli is composed of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku1285
更新日期:2015-01-01 00:00:00
abstract::How DNA sequence variation influences gene expression remains poorly understood. Diploid organisms have two homologous copies of their DNA sequence in the same nucleus, providing a rich source of information about how genetic variation affects a wealth of biochemical processes. However, few computational methods have ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz176
更新日期:2019-06-20 00:00:00
abstract::Explicit solvent molecular dynamics (MD) simulations were carried out for sarcin-ricin domain (SRD) motifs from 23S (Escherichia coli) and 28S (rat) rRNAs. The SRD motif consists of GAGA tetraloop, G-bulged cross-strand A-stack, flexible region and duplex part. Detailed analysis of the overall dynamics, base pairing, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkj470
更新日期:2006-02-02 00:00:00
abstract::The APOBEC3 proteins are unique to mammals. Many inhibit retrovirus infection through a cDNA cytosine deamination mechanism. HIV-1 neutralizes this host defense through Vif, which triggers APOBEC3 ubiquitination and degradation. Here, we report an APOBEC3F-like, double deaminase domain protein from three artiodactyls:...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl721
更新日期:2006-01-01 00:00:00
abstract::A peculiar phenomenon is observed in several adenovirus type 2 or 5 (Ad2 or Ad5) transformed cell lines: the right hand and left hand terminal regions of the viral genome present in the viral DNA insertions of these cell lines are found to be linked together. A large part of the viral DNA insertion present in the Ad5 ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.7.2189
更新日期:1982-04-10 00:00:00
abstract::In a bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP)/transcription factor binding screen, we identified Mycobacterium smegmatis Ms6479 as the first c-di-GMP-responsive transcriptional factor in mycobacteria. Ms6479 could specifically bind with c-di-GMP and recognize the promoters of 37 lipid transport an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks923
更新日期:2012-12-01 00:00:00
abstract::Guanine-rich sequences are highly abundant in the human genome, especially in regulatory regions. Because guanine-rich sequences have the unique ability to form G-quadruplexes, these structures may play a role in the regulation of gene transcription. In previous studies, we demonstrated that formation of G-quadruplexe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr259
更新日期:2011-09-01 00:00:00
abstract::Rad51 protein promotes homologous recombination in eukaryotes. Recombination activities are activated by Rad51 filament assembly on ssDNA. Previous studies of yeast Rad51 showed that His352 occupies an important position at the filament interface, where it could relay signals between subunits and active sites. To inve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq209
更新日期:2010-08-01 00:00:00
abstract::The covalent attachment of thiol-modified DNA oligomers; to self-assembled monolayer silane films on fused silica and oxidized silicon substrates is described. A heterobifunctional crosslinking molecule bearing both thiol- and amino-reactive moieties was used to tether a DNA oligomer (modified at its terminus with a t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.15.3031
更新日期:1996-08-01 00:00:00
abstract::Topoisomerase II, purified from chicken erythrocytes, was reacted with a large number of different DNA fragments and cleavages were catalogued in the presence and absence of drugs that stabilize the cleavage intermediate. Cleavages were sequenced to derive a consensus for topoisomerase II that predicts catalytic sites...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.12.5533
更新日期:1988-06-24 00:00:00
abstract::RNA exhibits a large diversity of conformations. Three thousand nucleotides of 23S and 5S ribosomal RNA from a structure of the large ribosomal subunit were analyzed in order to classify their conformations. Fourier averaging of the six 3D distributions of torsion angles and analyses of the resulting pseudo electron m...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh333
更新日期:2004-03-11 00:00:00
abstract::Conflicts between replication and transcription challenge chromosome duplication. Escherichia coli replisome movement along transcribed DNA is promoted by Rep and UvrD accessory helicases with Δrep ΔuvrD cells being inviable under rapid growth conditions. We have discovered that mutations in a tRNA gene, aspT, in an a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw1254
更新日期:2017-03-17 00:00:00