Abstract:
:The Bayesian regularization method for high-throughput differential analysis, described in Baldi and Long (A Bayesian framework for the analysis of microarray expression data: regularized t-test and statistical inferences of gene changes. Bioinformatics 2001: 17: 509-519) and implemented in the Cyber-T web server, is one of the most widely validated. Cyber-T implements a t-test using a Bayesian framework to compute a regularized variance of the measurements associated with each probe under each condition. This regularized estimate is derived by flexibly combining the empirical measurements with a prior, or background, derived from pooling measurements associated with probes in the same neighborhood. This approach flexibly addresses problems associated with low replication levels and technology biases, not only for DNA microarrays, but also for other technologies, such as protein arrays, quantitative mass spectrometry and next-generation sequencing (RNA-seq). Here we present an update to the Cyber-T web server, incorporating several useful new additions and improvements. Several preprocessing data normalization options including logarithmic and (Variance Stabilizing Normalization) VSN transforms are included. To augment two-sample t-tests, a one-way analysis of variance is implemented. Several methods for multiple tests correction, including standard frequentist methods and a probabilistic mixture model treatment, are available. Diagnostic plots allow visual assessment of the results. The web server provides comprehensive documentation and example data sets. The Cyber-T web server, with R source code and data sets, is publicly available at http://cybert.ics.uci.edu/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kayala MA,Baldi Pdoi
10.1093/nar/gks420subject
Has Abstractpub_date
2012-07-01 00:00:00pages
W553-9issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gks420journal_volume
40pub_type
杂志文章abstract::TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1043
更新日期:2007-01-01 00:00:00
abstract::DnaD and DnaB are essential DNA-replication-initiation proteins in low-G+C content Gram-positive bacteria. Here we use sensitive Hidden Markov Model-based techniques to show that the DnaB and DnaD proteins share a common structure that is evident across all their structural domains, termed DDBH1 and DDBH2 (DnaD DnaB H...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq465
更新日期:2010-11-01 00:00:00
abstract::ADAR enzymes, adenosine deaminases that act on RNA, form a family of RNA editing enzymes that convert adenosine to inosine within RNA that is completely or largely double-stranded. Site-selective A-->I editing has been detected at specific sites within a few structured pre-mRNAs of metazoans. We have analyzed the edit...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg681
更新日期:2003-08-15 00:00:00
abstract::Gene II protein is the only phage-encoded protein required for the double-stranded DNA replication of the distantly related filamentous phages IKe and Ff (M13, fd and f1). Complementation studies have demonstrated that, despite a significant degree of homology between the nucleotide sequences of the gene II's of IKe a...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.12.5067
更新日期:1986-06-25 00:00:00
abstract::For the rapid and sensitive detection of p53 'hot spot' mutations, we combined polymerase chain reaction based single-strand conformational polymorphism (PCR-SSCP) analysis with sequence specific-clamping by peptide nucleic acids (PNAs) in a one-step reaction tube protocol. For this purpose, we designed two PNA molecu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.5.1356
更新日期:1998-03-01 00:00:00
abstract::By successively assembling genetic parts such as BioBrick according to grammatical models, complex genetic constructs composed of dozens of functional blocks can be built. However, usually every category of genetic parts includes a few or many parts. With increasing quantity of genetic parts, the process of assembling...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx859
更新日期:2017-12-15 00:00:00
abstract::Aberration within the p53 tumor suppressor gene is the most frequently identified genetic damage in human cancer. Regulatory functions proposed for the p53 protein include modulation of the cell cycle, cellular differentiation, signal transduction, and gene expression. Additionally, the p53 gene product may guard the ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/21.3.713
更新日期:1993-02-11 00:00:00
abstract::An immunofluorescence assay was developed to identify proteins specifically binding to oligonucleoside phosphorodithioate (ODN) aptamers from a bead-bound ODN library. Accordingly, NF-kappaB p50 protein was incubated with either bead-bound NF-kappaB consensus sequence or a bead-bound ODN combinatorial library and adso...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng054
更新日期:2003-05-15 00:00:00
abstract::In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structure...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1133
更新日期:2015-12-02 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::The 'regions' method for multisequence alignment used in the previously reported program MALIGN has been generalized to include recursive refinement so that unaligned portions between two regions at the current level of resolution can be handled with increased resolution. Additionally, there is incorporated a limiting...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.5.1683
更新日期:1988-03-11 00:00:00
abstract::The σ subunit of bacterial RNA polymerase (RNAP) has been implicated in all steps of transcription initiation, including promoter recognition and opening, priming of RNA synthesis, abortive initiation and promoter escape. The post-promoter-recognition σ functions were proposed to depend on its conserved region σ3.2 th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1384
更新日期:2014-04-01 00:00:00
abstract::Rapid and transient activation of both c-fos transcription and mRNA accumulation occurs when resting CCL39 hamster fibroblasts are serum-stimulated to grow. By using several combinations of serum and cycloheximide, a protein synthesis inhibitor, we showed that: i) addition of cycloheximide to resting cell elicits an i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.14.5657
更新日期:1987-07-24 00:00:00
abstract::The pattern of sites for cleavage mediated by topoisomerase II was determined in 830 kb of cloned DNA from the Drosophila X chromosome, with the objectives of comparing it with mapped structural and functional landmarks and examining if the correlations with such landmarks reported in individual loci can be generalize...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.11.2041
更新日期:1997-06-01 00:00:00
abstract::The UAS (upstream activator sequence) of the yeast PGK gene contains a transcriptional activator domain located between bases -479 and -402 upstream from the initiating ATG. This region of the UAS contains three direct repeats of the sequence 5'CTTCC3'. The roles in transcriptional activation of these repeats and othe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.17.8245
更新日期:1988-09-12 00:00:00
abstract::We present a theory of pluralistic and stochastic gene regulation. To bridge the gap between empirical studies and mathematical models, we integrate pre-existing observations with our meta-analyses of the ENCODE ChIP-Seq experiments. Earlier evidence includes fluctuations in levels, location, activity, and binding of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw042
更新日期:2016-06-02 00:00:00
abstract::Bacterial genomics has revolutionized our understanding of the microbial tree of life; however, mapping and visualizing the distribution of functional traits across bacteria remains a challenge. Here, we introduce AnnoTree-an interactive, functionally annotated bacterial tree of life that integrates taxonomic, phyloge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz246
更新日期:2019-05-21 00:00:00
abstract::Deep mutational scanning has been used to create high-resolution DNA sequence maps that illustrate the functional consequences of large numbers of point mutations. However, this approach has not yet been applied to libraries of genes created by random circular permutation, an engineering strategy that is used to creat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky255
更新日期:2018-07-27 00:00:00
abstract::Biological and chemical DNA fragmentation generates DNA molecules with a variety of termini, including blunt ends and single-stranded overhangs. We have developed a Next Generation Sequencing (NGS) assay, XACTLY, to interrogate the termini of fragmented DNA, information traditionally lost in standard NGS library prepa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa128
更新日期:2020-05-07 00:00:00
abstract::Differential melting profiles and denaturation maps are calculated for fdDNA whose sequence of nucleotides has been determined recently. The melting profiles for the total DNA and a number of its restriction fragments are compared with experimental data taken from literature. The comparison enables one to correlate a ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/5.7.2547
更新日期:1978-07-01 00:00:00
abstract::Many DNA modification and repair enzymes require access to DNA bases and therefore flip nucleotides. Restriction endonucleases (REases) hydrolyze the phosphodiester backbone within or in the vicinity of the target recognition site and do not require base extrusion for the sequence readout and catalysis. Therefore, the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm513
更新日期:2007-01-01 00:00:00
abstract::The recognition of human tRNA(Leu) or tRNA(Ser) by cognate aminoacyl- tRNA synthetases has distinct requirements. Only one base change (A73-->G) in tRNA(Leu) is required to generate an efficient serine acceptor in vitro, whereas several changes in three structural domains (the acceptor stem, DHU loop and long extra ar...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.3.405
更新日期:1996-02-01 00:00:00
abstract::Since its discovery in 1979, left-handed Z-DNA has evolved from an in vitro curiosity to a challenging DNA structure with crucial roles in gene expression, regulation and recombination. A fundamental question that has puzzled researchers for decades is how the transition from B-DNA, the prevalent right-handed form of ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1003
更新日期:2013-01-07 00:00:00
abstract::A homogeneous nucleic acid hybridization assay which is conducted in solution and requires no separation steps is described. The assay is based on the concept of strand displacement. In the strand displacement assay, an RNA "signal strand" is hybridized within a larger DNA strand termed the "probe strand", which is, i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.17.6883
更新日期:1987-09-11 00:00:00
abstract::An important model system for studying the process leading to productive transcription is provided by the superfamily of nuclear receptors, which are for the most part ligand-controlled transcription factors. Over the past years several 'orphan' nuclear receptors have been isolated for which no ligand has yet been ide...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.16.3424
更新日期:2001-08-15 00:00:00
abstract::Ribosome assembly is a process fundamental for all cellular activities. The efficiency and accuracy of the subunit assembly are tightly regulated and closely monitored. In the present work, we characterized, both compositionally and structurally, a set of in vivo 50S subunit precursors (45S), isolated from a mutant ba...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt423
更新日期:2013-08-01 00:00:00
abstract::Mitochondrial-DNA diseases have no effective treatments. Allotopic expression-synthesis of a wild-type version of the mutated protein in the nuclear-cytosolic compartment and its importation into mitochondria-has been proposed as a gene-therapy approach. Allotopic expression has been successfully demonstrated in yeast...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq769
更新日期:2011-01-01 00:00:00
abstract::Addition of thiol compounds containing an anionic group to the 3'-terminal unsaturated sugar of the 5' fragment obtained from an oligonucleotide containing an AP site cleaved by beta-elimination, can be followed by gel electrophoresis. The technique enables to distinguish between two mechanisms of cleavage of the C3'-...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.20.9489
更新日期:1988-10-25 00:00:00
abstract::A requirement for specific RNA folding is that the free-energy landscape discriminate against non-native folds. While tertiary interactions are critical for stabilizing the native fold, they are relatively non-specific, suggesting additional mechanisms contribute to tertiary folding specificity. In this study, we use ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv1055
更新日期:2016-01-08 00:00:00
abstract::Apurinic/apyrimidinic endonuclease 1 (APE1), an essential protein in mammals, is involved in base excision DNA repair (BER) and in regulation of gene expression, acting as a redox co-activator of several transcription factors. Recent findings highlight a novel role for APE1 in RNA metabolism, which is modulated by nuc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq691
更新日期:2010-12-01 00:00:00