Abstract：
:One of the major issues in expression profiling analysis still is to outline proper thresholds to determine differential expression, while avoiding false positives. The problem being that the variance is inversely proportional to the log of signal intensities. Aiming to solve this issue, we describe a model, expression variation (EV), based on the LMS method, which allows data normalization and to construct confidence bands of gene expression, fitting cubic spline curves to the Box-Cox transformation. The confidence bands, fitted to the actual variance of the data, include the genes devoid of significant variation, and allow, based on the confidence bandwidth, to calculate EVs. Each outlier is positioned according to the dispersion space (DS) and a P-value is statistically calculated to determine EV. This model results in variance stabilization. Using two Affymetrix-generated datasets, the sets of differentially expressed genes selected using EV and other classical methods were compared. The analysis suggests that EV is more robust on variance stabilization and on selecting differential expression from both rare and strongly expressed genes.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Chuchana P,Marchand D,Nugoli M,Rodriguez C,Molinari N,Garcia-Sanz JAdoi
10.1093/nar/gkm093subject
Has Abstractpub_date
2007-01-01 00:00:00pages
e71issue
9eissn
0305-1048issn
1362-4962pii
gkm093journal_volume
35pub_type
杂志文章abstract：:Insertion of microRNA target sequences into the flavivirus genome results in selective tissue-specific attenuation and host-range restriction of live attenuated vaccine viruses. However, previous strategies for miRNA-targeting did not incorporate a mechanism to prevent target elimination under miRNA-mediated selective...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw061
更新日期：2016-04-20 00:00:00
abstract：:DNA predominantly contains Watson-Crick (WC) base pairs, but a non-negligible fraction of base pairs are in the Hoogsteen (HG) hydrogen bonding motif at any time. In HG, the purine is rotated ∼180° relative to the WC motif. The transitions between WC and HG may play a role in recognition and replication, but are diffi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz837
更新日期：2019-12-02 00:00:00
abstract：:In an extensive analysis, using a range of restriction endonucleases, HinfI and TaqI were found to differentiate satellites I, II and III & IV. Satellite I is resistant to digestion by TaqI, but is cleaved by HinfI to yield three major fragments of approximate size 770, 850 and 950bp, associated in a single length of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.2.547
更新日期：1982-01-22 00:00:00
abstract：:The tumor suppressor gene, p53, is rarely mutated in neuroblastomas (NB) at the time of diagnosis, but its dysfunction could result from a nonfunctional conformation or cytoplasmic sequestration of the wild-type p53 protein. However, p53 mutation, when it occurs, is found in NB tumors with drug resistance acquired ove...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl619
更新日期：2006-01-01 00:00:00
abstract：:We present a multi-laboratory effort to describe the structural and dynamical properties of duplex B-DNA under physiological conditions. By processing a large amount of atomistic molecular dynamics simulations, we determine the sequence-dependent structural properties of DNA as expressed in the equilibrium distributio...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz905
更新日期：2019-12-02 00:00:00
abstract：:In Saccharomyces cerevisiae the majority of the genes for 5S rRNA lie within a 9kb rDNA sequence that is present as 100-200 tandemly-repeated copies on Chromosome XII. Following our observations that about 10% of yeast 5S rRNA exists as minor variant sequences, we screened a collection of yeast DNA fragments cloned in...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.10.4083
更新日期：1984-05-25 00:00:00
abstract：:Early in its differentiative pathway, a given B lymphocyte expresses immunoglobulin of the mu heavy chain class (IgM). Subsequent differentiative processes may involve rearrangement within the immunoglobulin heavy chain chromosomal locus to enable cells of the same lineage to synthesize immunoglobulins of other heavy ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.1.225
更新日期：1985-01-11 00:00:00
abstract：:A new method which predicts internal exon sequences in human DNA has been developed. The method is based on a splice site prediction algorithm that uses the linear discriminant function to combine information about significant triplet frequencies of various functional parts of splice site regions and preferences of ol...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.24.5156
更新日期：1994-12-11 00:00:00
abstract：:Proteins that bind to DNA are found in all areas of genetic activity within the cell. To help understand how these proteins perform their various functions, it is useful to analyse which residues are involved in binding to the DNA and how they interact with the bases and sugar-phosphate backbone of nucleic acids. Here...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.24.4940
更新日期：1997-12-15 00:00:00
abstract：:We have investigated loop-induced structural perturbation of the stem structure in hairpins d(GAATTCXnGAATTC) (X = A, T and n = 3, 4, 5 and 6) that contain an EcoRI restriction site in close proximity to the hairpin loop. Oligonucleotides containing either a T3 or a A3 loop were not hydrolyzed by the restriction enzym...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.6.1489
更新日期：1990-03-25 00:00:00
abstract：:Thermally induced structural transition in the d(TTTTATAATAAA) d(TTTATTATAAAA) heteroduplex is characterized by UV-spectroscopy and differential scanning calorimetry. At low salt (less than 0.1 M) the occurrence of a cooperative transition in the lower temperature range, followed by a broad transition connected with s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.7.3245
更新日期：1984-04-11 00:00:00
abstract：:To gain insight into the mechanistic link between translation termination and nonsense-mediated mRNA decay (NMD), we depleted the ribosome recycling factor ABCE1 in human cells, resulting in an upregulation of NMD-sensitive mRNAs. Suppression of NMD on these mRNAs occurs prior to their SMG6-mediated endonucleolytic cl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa758
更新日期：2020-10-09 00:00:00
abstract：:The MPI Bioinformatics Toolkit (http://toolkit.tuebingen.mpg.de) is an open, interactive web service for comprehensive and collaborative protein bioinformatic analysis. It offers a wide array of interconnected, state-of-the-art bioinformatics tools to experts and non-experts alike, developed both externally (e.g. BLAS...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw348
更新日期：2016-07-08 00:00:00
abstract：:The PRISM web server enables fast and accurate prediction of protein-protein interactions (PPIs). The prediction algorithm is knowledge-based. It combines structural similarity and accounts for evolutionary conservation in the template interfaces. The predicted models are stored in its repository. Given two protein st...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku397
更新日期：2014-07-01 00:00:00
abstract：:Differences between species have been suggested to largely reside in the network of connections among the genes. Nevertheless, the rate at which these connections evolve has not been properly quantified. Here, we measure the extent to which co-regulation between pairs of genes is conserved over large phylogenetic dist...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkh815
更新日期：2004-09-07 00:00:00
abstract：:Comparison of the nucleotide sequence of mRNAs coding for several vertebrate actins revealed a high degree of sequence homology in the 3' untranslated region (3' UTR) between those mRNAs coding for homologous (isotypic) actins in different organisms but not between mRNAs coding for very similar isoforms differing in t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/13.10.3723
更新日期：1985-05-24 00:00:00
abstract：:Reversion of T type cytoplasmic male sterility (cmsT) to fertility is correlated with sequence changes in a 1.5 kb AvaI fragment. This 1.5 kb AvaI fragment is composed of 5' flanking sequences of ATPase subunit 6, one complete open reading frame (ORF 13) and part of the another (ORF 25). The sequence of the 1.5 kb Ava...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.15.6091
更新日期：1987-08-11 00:00:00
abstract：:Three clones containing both the human G gamma and A gamma globlin genes have been isolated and characterized from a library of DNA fragments generated by partial Eco RI digestion of cellular DNA using charon 4A phage as vector. Two of the clones (NY 2 and 3) are identical and have an insert of 14.0 kb. The third clon...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/7.5.1147
更新日期：1979-11-10 00:00:00
abstract：:Ribosomal RNA (rRNA) in intact ribosomes is cleaved into discrete products on incubation of reticulocyte lysates or L-cell extracts with ppp(A2'p)3A. Cleavage of rRNA may, therefore, provide a useful assay for 2-5A (ppp)A2'p)nA; n = 2 to 4) or for the presence of a 2-5A-dependent nuclease. The results with reticulocyt...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.7.1571
更新日期：1981-04-10 00:00:00
abstract：:Eukaryotic cellular mRNAs contain a cap at their 5'-ends, but some viral and cellular mRNAs bypass the cap-dependent mechanism of translation initiation in favor of internal entry of ribosomes at specific RNA sequences. Cap-dependent initiation requires intact initiation factor eIF4G (formerly eIF-4gamma, eIF-4Fgamma ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.2.395
更新日期：1997-01-15 00:00:00
abstract：:Locked nucleic acid (LNA) is a chemically modified nucleic acid with its sugar ring locked in an RNA-like (C3'-endo) conformation. LNAs show extraordinary thermal stabilities when hybridized with DNA, RNA or LNA itself. We performed molecular dynamics simulations on five isosequential duplexes (LNA-DNA, LNA-LNA, LNA-R...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1182
更新日期：2008-03-01 00:00:00
abstract：:Recent advances in next-generation sequencing technologies and genome assembly algorithms have enabled the accumulation of a huge volume of genome sequences from various species. This has provided new opportunities for large-scale comparative genomics studies. Identifying and utilizing synteny blocks, which are genomi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw310
更新日期：2016-07-08 00:00:00
abstract：:Proteins are highly dynamic molecules, whose function is intrinsically linked to their molecular motions. Despite the pivotal role of protein dynamics, their computational simulation cost has led to most structure-based approaches for assessing the impact of mutations on protein structure and function relying upon sta...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky300
更新日期：2018-07-02 00:00:00
abstract：:A rearrangement of the mitochondrial genome of a long lived mutant of Podospora anserina is presented. It consists in the insertion of 191 bp of the LrDNA gene (coding for the large ribosomal RNA) at the junction between exon1 and intron alpha of gene co1 (coding for subunit 1 of cytochrome oxidase). This insertion is...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.4.779
更新日期：1990-02-25 00:00:00
abstract：:The RNA Editing Database (REDIdb) is an interactive, web-based database created and designed with the aim to allocate RNA editing events such as substitutions, insertions and deletions occurring in a wide range of organisms. The database contains both fully and partially sequenced DNA molecules for which editing infor...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl793
更新日期：2007-01-01 00:00:00
abstract：:We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet. The web portal offers convenient interactive access to a growing pool of chainable bioinformatics software tools and databases that are centrally installed and maintained by the RZG. Cur...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl254
更新日期：2006-07-01 00:00:00
abstract：:Highly toxic DNA double-strand breaks (DSBs) readily trigger the DNA damage response (DDR) in cells, which delays cell cycle progression to ensure proper DSB repair. In Saccharomyces cerevisiae, mitotic S phase (20-30 min) is lengthened upon DNA damage. During meiosis, Spo11-induced DSB onset and repair lasts up to 5 ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa587
更新日期：2020-09-04 00:00:00
abstract：:The polymerase encoded by human hepatitis B virus, which has reverse transcriptase and RNase H activity, binds to its pregenomic RNA template in a two-step process involving a terminal redundancy. Both first strand and second strand DNA synthesis involve primer translocation and second strand synthesis involves a temp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.17.3295
更新日期：1996-09-01 00:00:00
abstract：:A 9.2 kb segment of the maxi-circle of Trypanosoma brucei mitochondrial DNA contains the genes for cytochrome c oxidase subunits I and II (coxI and coxII) and seven Unassigned Reading Frames ("URFs"). The genes for coxI and coxII display considerable homology at the aminoacid level (38 and 25%, respectively) to the co...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.19.7327
更新日期：1984-10-11 00:00:00
abstract：:A new integrated image analysis package with quantitative quality control schemes is described for cDNA microarray technology. The package employs an iterative algorithm that utilizes both intensity characteristics and spatial information of the spots on a microarray image for signal-background segmentation and define...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.15.e75
更新日期：2001-08-01 00:00:00
