Abstract:
:ADGO 2.0 is a web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. Some other tools also incorporate composite annotations solely for interpreting lists of genes but usually provide highly redundant information. This new version has the following additional features: first, it provides multiple gene set analysis methods for microarray inputs as well as enrichment analyses for lists of genes. Second, it screens redundant composite annotations when generating and prioritizing them. Third, it incorporates union and subtracted sets as well as intersection sets. Lastly, users can upload their own gene sets (e.g. predicted miRNA targets) to generate and analyze new composite sets. The first two features are unique to ADGO 2.0. Using our tool, we demonstrate analyses of a microarray dataset and a list of genes for T-cell differentiation. The new ADGO is available at http://www.btool.org/ADGO2.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Chi SM,Kim J,Kim SY,Nam Ddoi
10.1093/nar/gkr392subject
Has Abstractpub_date
2011-07-01 00:00:00pages
W302-6issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkr392journal_volume
39pub_type
杂志文章abstract::Preparation of the two nonanucleotides, d(pG-G-A-G-G-A-G-A-A) and d(pT-T-C-T-G-T-T-G-A), and the octanucleotide, d(pT-G-G-C-C-C-A-T) is described by a rapid solid-phase method on a polyamide support. The syntheses were carried out using a modified solid-phase peptide synthesiser and required one day for each nucleotid...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.12.4391
更新日期:1977-12-01 00:00:00
abstract::Many strains of E. coli K12 restrict DNA containing cytosine methylation such as that present in plant and animal genomes. Such restriction can severely inhibit the efficiency of cloning genomic DNAs. We have quantitatively evaluated a total of 39 E. coli strains for their tolerance to cytosine methylation in phage an...
journal_title:Nucleic acids research
pub_type: 杂志文章
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abstract::The unknown modified nucleotide G*, isolated from both Schizosaccharomyces pombe and Torulopsis utilis initiator tRNAs(Met), has been identified as an O-ribosyl-(1"----2')-guanosine-5"-phosphate, called Gr(p), by means of HPLC, UV-absorption, mass spectrometry and periodate oxidation procedures. By comparison with the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.19.5199
更新日期:1991-10-11 00:00:00
abstract::Horizontally acquired genes are typically regulated by ancestral regulators. This regulation enables expression of horizontally acquired genes to be coordinated with that of preexisting genes. Here, we report a singular example of the opposite regulation: a horizontally acquired gene that controls an ancestral regulat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa813
更新日期:2020-11-04 00:00:00
abstract::Synthesis and radioiodination of a stannyl oligodeoxyribonucleotide were undertaken to evaluate a gamma ray emitting ODN ligand for thrombus imaging in vivo . Synthesis of the ODN was based on modified automatedbeta-cyanoethyl phosphoramidite chemistry with an organotin nucleoside (dU*) coupled to a thrombin binding a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.14.2897
更新日期:1997-07-15 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
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abstract::Transcription factor decoy binding sites are short DNA sequences that can titrate a transcription factor away from its natural binding site, therefore regulating gene expression. In this study, we harness synthetic transcription factor decoy systems to regulate gene expression for metabolic pathways in Escherichia col...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1234
更新日期:2021-01-25 00:00:00
abstract::In fission yeast and other eukaryotes, Rec12 (Spo11) is thought to catalyze the formation of dsDNA breaks (DSBs) that initiate homologous recombination in meiosis. Rec12 is orthologous to the catalytic subunit of topoisomerase VI (Top6A). Guided by the crystal structure of Top6A, we engineered the rec12 locus to encod...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq993
更新日期:2011-03-01 00:00:00
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journal_title:Nucleic acids research
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更新日期:2001-01-01 00:00:00
abstract::Earlier we have shown that exogenous expression of HIPPI, a molecular partner of Huntingtin interacting protein HIP-1, induces apoptosis and increases expression of caspases-1, -8 and -10 in HeLa and Neuro2A cells. The C-terminal pseudo death effector domain of HIPPI (pDED-HIPPI) specifically interacts with the putati...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1011
更新日期:2010-01-01 00:00:00
abstract::Accurate maps and DNA sequences for human subtelomere regions, along with detailed knowledge of subtelomere variation and long-range telomere-terminal haplotypes in individuals, are critical for understanding telomere function and its roles in human biology. Here, we use a highly automated whole genome mapping technol...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx017
更新日期:2017-05-19 00:00:00
abstract::We studied in vivo transcription and gene expression directed by a series of synthetic sequences, bearing the consensus hexamer (CH) pair of E.coli promoters in various contexts. The results demonstrate that, for the contexts tested, the CH pair supports transcription activity and gene expression, whether the spacer l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.5.1137
更新日期:1990-03-11 00:00:00
abstract::Sequences preceding the minimal promoter play a role in the differential expression of the Xenopus somatic and oocyte-type 5S RNA genes. In this report, the somatic sequences between -32 and +37 are shown to increase transcriptional activity in microinjected embryos, yet have little to no effect in microinjected oocyt...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:
更新日期:1989-11-25 00:00:00
abstract::We have previously reported that transcription from a distal promoter (promoter B) of the estrogen receptor alpha (ERalpha) gene is responsible for the increased expression of ERalpha in human breast carcinomas. This paper first characterized the promoter B region in terms of transient transfection experiments with lu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.3.903
更新日期:1999-02-01 00:00:00
abstract::T4 polynucleotide kinase (Pnk) is a bifunctional 5'-kinase/3'-phosphatase that aids in the repair of broken termini in RNA by converting 3'-PO4/5'-OH ends into 3'-OH/5'-PO4 ends, which are then sealed by RNA ligase. Here we have employed site-directed mutagenesis (introducing 31 mutations at 16 positions) to locate ca...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.4.1073
更新日期:2002-02-15 00:00:00
abstract::The advent of jellyfish green fluorescent protein and its spectral variants, together with promising new fluorescent proteins from other classes of the Cnidarian phylum (coral and anemones), has greatly enhanced and promises to further boost the detection and localization of proteins in cell biology. It has been less ...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/29.5.1013
更新日期:2001-03-01 00:00:00
abstract::The determination of distances between specific points in nucleic acids is essential to understanding their behaviour at the molecular level. The ability to measure distances of 2-10 nm is particularly important: deformations arising from protein binding commonly fall within this range, but the reliable measurement of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa086
更新日期:2020-04-06 00:00:00
abstract::Ribosomal protein L11 and its associated binding site on 23S rRNA together comprise one of the principle components that mediate interactions of translation factors with the ribosome. This site is also the target of the antibiotic thiostrepton, which has been proposed to act by preventing important structural transiti...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh644
更新日期:2004-06-15 00:00:00
abstract::When averaged over the full yeast protein-protein interaction and transcriptional regulatory networks, protein hubs with many interaction partners or regulators tend to evolve significantly more slowly due to increased negative selection. However, genome-wide analysis of protein evolution in the subnetworks of associa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq353
更新日期:2010-10-01 00:00:00
abstract::About 40% of the genes in the nematode Caenorhabditis elegans have homologs in humans. Based on the history of this model system, it is clear that the application of genetic methods to the study of this set of genes would provide important clues to their function in humans. To facilitate such genetic studies, we are e...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnf051
更新日期:2002-06-15 00:00:00
abstract::We demonstrate a single DNA molecule optical mapping assay able to resolve a specific Escherichia coli strain from other strains. The assay is based on competitive binding of the fluorescent dye YOYO-1 and the AT-specific antibiotic netropsin. The optical map is visualized by stretching the DNA molecules in nanofluidi...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2014-09-01 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2011-09-01 00:00:00
abstract::Mitome is a specialized mitochondrial genome database designed for easy comparative analysis of various features of metazoan mitochondrial genomes such as base frequency, A+T skew, codon usage and gene arrangement pattern. A particular function of the database is the automatic reconstruction of phylogenetic relationsh...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm763
更新日期:2008-01-01 00:00:00
abstract::Human immunodeficiency virus type 2 (HIV-2) reverse transcription is initiated from cellular tRNA(Lys3) partially annealed to the RNA viral genome at the primer binding site (PBS). This annealing involves interactions between two highly structured RNA molecules. In contrast to HIV-1, in which the reverse transcription...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.13.2757
更新日期:2001-07-01 00:00:00
abstract::Glutaminyl-tRNA synthetase from Deinococcus radiodurans possesses a C-terminal extension of 215 residues appending the anticodon-binding domain. This domain constitutes a paralog of the Yqey protein present in various organisms and part of it is present in the C-terminal end of the GatB subunit of GatCAB, a partner of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1164
更新日期:2007-01-01 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::We have developed a highly sensitive method for DNA analysis on 3D gel element microarrays, a technique we call multiplex microarray-enhanced PCR (MME-PCR). Two amplification strategies are carried out simultaneously in the reaction chamber: on or within gel elements, and in bulk solution over the gel element array. M...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2005-01-20 00:00:00
abstract::Mitochondrial aprataxin (APTX) protects the mitochondrial genome from the consequence of ligase failure by removing the abortive ligation product, i.e. the 5'-adenylate (5'-AMP) group, during DNA replication and repair. In the absence of APTX activity, blocked base excision repair (BER) intermediates containing the 5'...
journal_title:Nucleic acids research
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更新日期:2017-09-29 00:00:00
abstract::Repression of cellular reprogramming in germ cells is critical to maintaining cell fate and fertility. When germ cells mis-express somatic genes they can be directly converted into other cell types, resulting in loss of totipotency and reproductive potential. Identifying the molecular mechanisms that coordinate these ...
journal_title:Nucleic acids research
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更新日期:2020-05-07 00:00:00
abstract::Silencing gene expression by siRNAs is rapidly becoming a powerful tool for the genetic analysis of mammalian cells. However, the rapid degradation of siRNA and the limited duration of its action call for an efficient delivery technology. Accordingly, we describe here that Atelocollagen complexed with siRNA is resista...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh093
更新日期:2004-07-22 00:00:00