Abstract:
:KUPS (The University of Kansas Proteomics Service) provides high-quality protein-protein interaction (PPI) data for researchers developing and evaluating computational models for predicting PPIs by allowing users to construct ready-to-use data sets of interacting protein pairs (IPPs), non-interacting protein pairs (NIPs) and associated features. Multiple filters and options allow the user to control the make-up of the IPPs and NIPs as well as the quality of the resultant data sets. Each data set is built from the overall database, which includes 185 446 IPPs and ∼1.5 billion NIPs from five primary databases: IntAct, HPRD, MINT, UniProt and the Gene Ontology. The IPP set can be set to specific model organisms, interaction types and experimental evidence. The NIP set can be generated using four different strategies, which can alleviate biased estimation problems. Lastly, multiple features can be provided for all of the IPP and NIP pairs. Additionally, KUPS provides two benchmark data sets to help researchers compare their algorithms to existing approaches. KUPS is freely available at http://www.ittc.ku.edu/chenlab.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Chen XW,Jeong JC,Dermyer Pdoi
10.1093/nar/gkq943subject
Has Abstractpub_date
2011-01-01 00:00:00pages
D750-4issue
Database issueeissn
0305-1048issn
1362-4962pii
gkq943journal_volume
39pub_type
杂志文章abstract::The Gene Expression Atlas (http://www.ebi.ac.uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp936
更新日期:2010-01-01 00:00:00
abstract::Transcript of the rbpA1 gene in Anabaena variabilis accumulates significantly at low growth temperatures below 28 degreesC. This accumulation was maximal at 16 degreesC. Accumulation of the rbpA1 transcript was completely abolished by rifampicin, but not by chloramphenicol. Photosynthesis was not required for this col...
journal_title:Nucleic acids research
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doi:10.1093/nar/26.9.2192
更新日期:1998-05-01 00:00:00
abstract::Alternative RNA splicing is an essential process to yield proteomic diversity in eukaryotic cells, and aberrant splicing is often associated with numerous human diseases and cancers. We recently described serine/arginine-rich splicing factor 3 (SRSF3 or SRp20) being a proto-oncogene. However, the SRSF3-regulated splic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1500
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abstract::Several mono-, di-, tetra-, penta- and nonaribozymes were developed. These multitarget-ribozymes were targeted to cleave HIV-1 env RNA at up to nine different conserved sites. Each multitarget-ribozyme consisted of a chain of up to nine hammerhead motifs, each flanked by a different targeting sequence. The multitarget...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.17.4581
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abstract::We report here the discovery of HMBP, a protein in nuclei of human T-helper lymphocytes and other human cell types, which binds with enhanced affinity to a promoter element in the HIV-1 long terminal repeat when that element is methylated at CpGs, the target site of the human DNA methyltransferase. This promoter eleme...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.24.5786
更新日期:1993-12-11 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
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abstract::Recent studies show that the region of DNA brought into close proximity to the fetal gamma-globin genes in deletional forms of hereditary persistence of fetal hemoglobin (HPFH) is selectively hypomethylated (and presumably active) in normal erythroid tissue. This region is normally located approximately 100 kilobases ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.13.5169
更新日期:1987-07-10 00:00:00
abstract::The role of TATA elements in the expression of a mammalian promoter was investigated in the fission yeast Schizosaccharomyces pombe, by studying the human adenovirus E2-early promoter. This is a unique dual promoter with two nonconsensus TATA elements directing transcription from two cap sites, +1 and -26. A sequence ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.11.2737
更新日期:1993-06-11 00:00:00
abstract::Thymine DNA glycosylase (TDG) is a DNA repair enzyme that excises a variety of mismatched or damaged nucleotides (nts), e.g. dU, dT, 5fC and 5caC. TDG is shown to play essential roles in maintaining genome integrity and correctly programming epigenetic modifications through DNA demethylation. After locating the lesion...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky386
更新日期:2018-06-20 00:00:00
abstract::The multiprotein complexes involved in active dis-ruption of chromatin structure, homologous to yeast SWI/SNF complex, have been described for human and Drosophila cells. In all SWI/SNF-class complexes characterised so far, one of the key components is the SNF5-type protein. Here we describe the isolation of a plant (...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.11.2393
更新日期:1999-06-01 00:00:00
abstract::The mouse c-Ki-ras protooncogene promoter contains an unusual DNA element consisting of a 27 bp-long homopurine-homopyrimidine mirror repeat (H-motif) adjacent to a d(C-G)5 repeat. We have previously shown that in vitro these repeats may adopt H and Z conformations, respectively, causing nuclease and chemical hypersen...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.16.3271
更新日期:1994-08-25 00:00:00
abstract::Acetyl-CoA Carboxylase catalyzes the first committed step in fatty acid synthesis. Escherichia coli acetyl-CoA carboxylase is composed of biotin carboxylase, carboxyltransferase and biotin carboxyl carrier protein functions. The accA and accD genes that code for the alpha- and beta-subunits, respectively, are not in a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp1079
更新日期:2010-03-01 00:00:00
abstract::Two hexamer DNA fragments containing a carcinogenic modified base, O6-methyl guanine, have been synthesized by a solid-phase phosphotriester method, in which the unmodified guanine residues present were O6 protected with the 4-nitrophenylethyl group. These two alkylated oligonucleotides were found to have similar Tm's...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.10.3393
更新日期:1983-05-25 00:00:00
abstract::ATRX and MeCP2 belong to an expanding group of chromatin-associated proteins implicated in human neurodevelopmental disorders, although their gene-regulatory activities are not fully resolved. Loss of ATRX prevents full repression of an imprinted gene network in the postnatal brain and in this study we address the mec...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku564
更新日期:2014-07-01 00:00:00
abstract::In Saccharomyces cerevisiae, the stability of highly repetitive rDNA array is maintained through transcriptional silencing. Recently, a β-1,3-glucanosyltransferase Gas1 has been shown to play a significant role in the regulation of transcriptional silencing in S. cerevisiae. Here, we show that the gas1Δ mutation incre...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku570
更新日期:2014-07-01 00:00:00
abstract::Eukaryotic tRNAs are transcribed as precursors. A 5'-end leader and 3'-end trailer are endonucleolytically removed by RNase P and 3'-tRNase before 3'-end CCA addition, aminoacylation, nuclear export and translation. 3'-End -CC can be a 3'-tRNase anti-determinant with the ability to prevent mature tRNA from recycling t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.21.4334
更新日期:2001-11-01 00:00:00
abstract::The large terminase subunit is a central component of the genome packaging motor from tailed bacteriophages and herpes viruses. This two-domain enzyme has an N-terminal ATPase activity that fuels DNA translocation during packaging and a C-terminal nuclease activity required for initiation and termination of the packag...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks974
更新日期:2013-01-07 00:00:00
abstract::The effects of Mg++, Mn++, and KCl addition, individually and in combination, on the rate of DNA- and RNA-primed DNA synthesis by avian myeloblastosis virus DNA polymerase (reverse transcriptase) using a variety of natural and synthetic template-primer combinations were examined. Optimal divalent cation concentrations...
journal_title:Nucleic acids research
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更新日期:1976-06-01 00:00:00
abstract::The mutL and mutS genes of Vibrio cholerae have been identified using interspecific complementation of Escherichia coli mutL and mutS mutants with plasmids containing the gene bank of V. cholerae. The recombinant plasmid pJT470, containing a 4.7 kb fragment of V. cholerae DNA codes for a protein of molecular weight 92...
journal_title:Nucleic acids research
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更新日期:1989-08-11 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
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abstract::PCAF and hGCN5 are distinct human genes that encode proteins related to the yeast histone acetyltransferase and transcriptional adapter GCN5. The PCAF protein shares extensive similarity with the 439 amino acids of yGCN5, but it has an approximately 350 amino acid N-terminal extension that interacts with the transcrip...
journal_title:Nucleic acids research
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更新日期:1998-06-15 00:00:00
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journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks395
更新日期:2012-09-01 00:00:00
abstract::Resistance to androgen receptor (AR)-targeted therapies in prostate cancer (PC) is a major clinical problem. A key mechanism of treatment resistance in advanced PC is the generation of alternatively spliced forms of the AR termed AR variants (AR-Vs) that are refractory to targeted agents and drive tumour progression. ...
journal_title:Nucleic acids research
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doi:10.1093/nar/gkz286
更新日期:2019-06-20 00:00:00
abstract::Regulatory T-cells (Treg) play an essential role in the negative regulation of immune answers by developing an attenuated cytokine response that allows suppressing proliferation and effector function of T-cells (CD4(+) Th). The transcription factor FoxP3 is responsible for the regulation of many genes involved in the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
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更新日期:2011-10-01 00:00:00
abstract::The prime mechanism by which p53 acts as a tumor suppressor is as a transcription factor regulating the expression of diverse downstream genes. The DNA-binding domain of p53 (p53DBD) interacts with defined DNA sites and is the main target for mutations in human primary tumors. Here, we show that the CWWG motif, found ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1044
更新日期:2011-03-01 00:00:00
abstract::A simple and effective modified ethanol precipitation-based protocol is described for the preparation of DNA from ancient human bones. This method is fast and requires neither hazardous chemicals nor special devices. After the powdering and incubating of the bone samples Dextran Blue was added as a carrier for removin...
journal_title:Nucleic acids research
pub_type: 历史文章,杂志文章
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更新日期:2000-06-15 00:00:00
abstract::Thousands of eukaryotic protein-coding genes generate circular RNAs that have covalently linked ends and are resistant to degradation by exonucleases. To prove their circularity as well as biochemically enrich these transcripts, it has become standard in the field to use the 3'-5' exonuclease RNase R. Here, we demonst...
journal_title:Nucleic acids research
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更新日期:2019-09-19 00:00:00
abstract::Genetic recombination in meiosis plays an important role in generating diversity of genetic information. In yeast an Escherichia coli RecA-like gene, DMC1, is expressed in meiotic prophase and its product co-localizes with Rad51 protein on zygotene chromosomes. We have cloned the mouse and human homologs of the yeast ...
journal_title:Nucleic acids research
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更新日期:1996-02-01 00:00:00
abstract::Exome sequencing strategy is promising for finding novel mutations of human monogenic disorders. However, pinpointing the casual mutation in a small number of samples is still a big challenge. Here, we propose a three-level filtration and prioritization framework to identify the casual mutation(s) in exome sequencing ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1257
更新日期:2012-04-01 00:00:00
abstract::Current DNA assembly methods for preparing highly purified linear subassemblies require complex and time-consuming in vitro manipulations that hinder their ability to construct megabase-sized DNAs (e.g. synthetic genomes). We have developed a new method designated 'CasHRA (Cas9-facilitated Homologous Recombination Ass...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw475
更新日期:2016-08-19 00:00:00