Abstract：
:In two-colour microarrays, the ratio of signal intensities of two co-hybridized samples is used as a relative measure of gene expression. Ratio-based analysis becomes complicated and inefficient in multi-class comparisons. We therefore investigated the validity of an intensity-based analysis procedure. To this end, two different cRNA targets were hybridized together, separately, with a common reference and in a self-self fashion on spotted 65mer oligonucleotide microarrays. We found that the signal intensity of the cRNA targets was not influenced by the presence of a target labelled in the opposite colour. This indicates that targets do not compete for binding sites on the array, which is essential for intensity-based analysis. It is demonstrated that, for good-quality arrays, the correlation of signal intensity measurements between the different hybridization designs is high (R > 0.9). Furthermore, ratio calculations from ratio- and intensity-based analyses correlated well (R > 0.8). Based on these results, we advocate the use of separate intensities rather than ratios in the analysis of two-colour long-oligonucleotide microarrays. Intensity-based analysis makes microarray experiments more efficient and more flexible: It allows for direct comparisons between all hybridized samples, while circumventing the need for a reference sample that occupies half of the hybridization capacity.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
't Hoen PA,Turk R,Boer JM,Sterrenburg E,de Menezes RX,van Ommen GJ,den Dunnen JTdoi
10.1093/nar/gnh038keywords:
subject
Has Abstractpub_date
2004-02-24 00:00:00pages
e41issue
4eissn
0305-1048issn
1362-4962pii
32/4/e41journal_volume
32pub_type
杂志文章abstract：:2'-O-Aminooxymethyl ribonucleosides are prepared from their 3',5'-disilylated 2'-O-phthalimidooxymethyl derivatives by treatment with NH(4)F in MeOH. The reaction of these novel ribonucleosides with 1-pyrenecarboxaldehyde results in the efficient formation of stable and yet reversible ribonucleoside 2'-conjugates in y...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr896
更新日期：2012-03-01 00:00:00
abstract：:Sequencing of RNAs (RNA-Seq) has revolutionized the field of transcriptomics, but the reads obtained often contain errors. Read error correction can have a large impact on our ability to accurately assemble transcripts. This is especially true for de novo transcriptome analysis, where a reference genome is not availab...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt215
更新日期：2013-05-01 00:00:00
abstract：:Histone H2A ubiquitination plays critical roles in transcriptional repression and deoxyribonucleic acid (DNA) damage response. More attention has been focused on ubiquitin E3 ligases of H2A, however, less is known about the negative regulators of H2A ubiquitination. Here we identified HSCARG as a new negative regulato...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku230
更新日期：2014-05-01 00:00:00
abstract：:This paper presents TurboFold II, an extension of the TurboFold algorithm for predicting secondary structures for multiple RNA homologs. TurboFold II augments the structure prediction capabilities of TurboFold by additionally providing multiple sequence alignments. Probabilities for alignment of nucleotide positions b...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx815
更新日期：2017-11-16 00:00:00
abstract：:Archival formalin-fixed, paraffin-embedded and ethanol-fixed tissues represent a potentially invaluable resource for gene expression analysis, as they are the most widely available material for studies of human disease. Little data are available evaluating whether RNA obtained from fixed (archival) tissues could produ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.2.e4
更新日期：2002-01-15 00:00:00
abstract：:We characterised the human hSuv3p protein belonging to the family of NTPases/helicases. In yeast mitochondria the hSUV3 orthologue is a component of the degradosome complex and participates in mtRNA turnover and processing, while in Caenorhabditis elegans the hSUV3 orthologue is necessary for viability of early embryo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkf647
更新日期：2002-12-01 00:00:00
abstract：:FASTQ has emerged as a common file format for sharing sequencing read data combining both the sequence and an associated per base quality score, despite lacking any formal definition to date, and existing in at least three incompatible variants. This article defines the FASTQ format, covering the original Sanger stand...
journal_title：Nucleic acids research
pub_type： 历史文章,杂志文章,评审
doi：10.1093/nar/gkp1137
更新日期：2010-04-01 00:00:00
abstract：:The tissue specificity of mitochondrial tRNA mutations remains largely elusive. In this study, we demonstrated the deleterious effects of tRNAThr 15927G>A mutation that contributed to pathogenesis of coronary artery disease. The m.15927G>A mutation abolished the highly conserved base-pairing (28C-42G) of anticodon ste...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky1241
更新日期：2019-02-28 00:00:00
abstract：:Formation of a transcriptionally competent open complex is a highly regulated multistep process involving at least two intermediates. The rate of formation and stability of the intermediate complexes often determine promoter strength. However, the detailed mechanism of formation of the open complex and the high resolu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.3.854
更新日期：2001-02-01 00:00:00
abstract：:Nonsense-mediated mRNA decay (NMD) is a molecular pathway of mRNA surveillance that ensures rapid degradation of mRNAs containing premature translation termination codons (PTCs) in eukaryotes. NMD has been shown to also regulate normal gene expression and thus emerged as one of the key post-transcriptional mechanisms ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm461
更新日期：2007-01-01 00:00:00
abstract：:IL-2 gene expression in activated T-cells is initiated by chromatin remodeling at the IL-2 proximal promoter and conversion of a transcriptional repressor into a potent transcriptional activator. A purine-box regulator complex was purified from activated Jurkat T-cell nuclei based on sequence-specific DNA binding to t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm117
更新日期：2007-01-01 00:00:00
abstract：:The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the primary community model organism database for the laboratory mouse and serves as the source for key biological reference data related to mouse genes, gene functions, phenotypes and disease models with a strong emphasis on the relationship of these ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1211
更新日期：2016-01-04 00:00:00
abstract：:We present RADAR--a rigorously annotated database of A-to-I RNA editing (available at http://RNAedit.com). The identification of A-to-I RNA editing sites has been dramatically accelerated in the past few years by high-throughput RNA sequencing studies. RADAR includes a comprehensive collection of A-to-I RNA editing si...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt996
更新日期：2014-01-01 00:00:00
abstract：:The availability of a draft human genome sequence and ability to monitor the transcription of thousands of genes with DNA microarrays has necessitated the need for new computational tools that can analyze cis-regulatory elements controlling genes that display similar expression patterns. We have developed a tool desig...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnf120
更新日期：2002-11-01 00:00:00
abstract：:Mature chicken erythrocyte polynucleosomes which are soluble at physiological ionic strength are enriched in beta-globin DNA sequences. Vitellogenin chromatin, which is not expressed in this tissue, is found in aggregation prone, salt insoluble chromatin. There is a direct correlation between the size of soluble fragm...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/15.3.1081
更新日期：1987-02-11 00:00:00
abstract：:A comprehensive listing is made of posttranscriptionally modified nucleosides from RNA reported in the literature through mid-1994. Included are chemical structures, common names, symbols, Chemical Abstracts registry numbers (for ribonucleoside and corresponding base), Chemical Abstracts Index Name, phylogenetic sourc...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/22.12.2183
更新日期：1994-06-25 00:00:00
abstract：:Alternative splicing of pre-mRNA generates protein diversity. Dysfunction of splicing machinery and expression of specific transcripts has been linked to cancer progression and drug response. Exon microarray technology enables genome-wide quantification of expression levels of the majority of exons and facilitates the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr513
更新日期：2011-10-01 00:00:00
abstract：:The HUGO Gene Nomenclature Committee (HGNC) based at EMBL's European Bioinformatics Institute (EMBL-EBI) assigns unique symbols and names to human genes. There are over 42,000 approved gene symbols in our current database of which over 19 000 are for protein-coding genes. While we still update placeholder and problema...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa980
更新日期：2021-01-08 00:00:00
abstract：:By means of a combination of ion-exchange and sequence-specific affinity chromatography techniques, we have purified to homogeneity two protein complexes binding in a human DNA region (B48) previously recognized to contain a DNA replication origin. The DNA sequence used for the protein purification (B48 binding site) ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/21.14.3257
更新日期：1993-07-11 00:00:00
abstract：:Chromatin boundaries regulate gene expression by modulating enhancer-promoter interactions and insulating transcriptional influences from organized chromatin. However, mechanistic distinctions between these two aspects of boundary function are not well understood. Here we show that SF1, a chromatin boundary located in...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp362
更新日期：2009-07-01 00:00:00
abstract：:Programmed chromosome breakage occurs at 50-200 specific sites in the genome of Tetrahymena thermo-phila during somatic nuclear (macronuclear) differentiation. Previous studies have identified a 15 bp sequence, the Cbs (for chromosome breakage sequence), that is necessary and sufficient to specify these sites. In this...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.4.895
更新日期：2000-02-15 00:00:00
abstract：:AR9 is a giant Bacillus subtilis phage whose uracil-containing double-stranded DNA genome encodes distant homologs of β and β' subunits of bacterial RNA polymerase (RNAP). The products of these genes are thought to assemble into two non-canonical multisubunit RNAPs - a virion RNAP (vRNAP) that is injected into the hos...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx264
更新日期：2017-06-02 00:00:00
abstract：:Using a powerful computer-assisted analysis strategy, a large-scale search of small nucleolar RNA (snoRNA) genes in the recently released draft sequence of the rice genome was carried out. This analysis identified 120 different box C/D snoRNA genes with a total of 346 gene variants, which were predicted to guide 135 2...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg373
更新日期：2003-05-15 00:00:00
abstract：:Myocyte enhancer binding factor 2 (MEF2) proteins belong to the MADS box family of transcription factors and four MEF2 proteins, MEF2A, MEF2B, MEF2C and MEF2D, have been found. MEF2 proteins have been shown to play critical roles in differentiation of muscles and neuronal tissues. How transactivational activity of MEF...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.13.2836
更新日期：2001-07-01 00:00:00
abstract：:Modification of cytosine plays an important role in epigenetic regulation of gene expression and genome stability. Cytosine is converted to 5-methylcytosine (5mC) by DNA methyltransferase; in turn, 5mC may be oxidized to 5-hydroxymethylcytosine (5hmC) by ten-eleven translocation enzyme. The structural flexibility of D...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa1210
更新日期：2021-01-25 00:00:00
abstract：:Infection of Escherichia coli by a bacteriophage T4 regA, gene 44 double mutant leads to about a 7-fold increase in the amount of RNA ligase obtained after infection by wild-type phage. Using cells infected by the double mutant, RNA ligase was purified to homogeneity with a 20% yield. Unlike previous preparations of t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.9.3175
更新日期：1977-09-01 00:00:00
abstract：:Most microbes have not been cultured, and many of those that are cultivatable are difficult, dangerous or expensive to propagate or are genetically intractable. Routine cloning of large genome fractions or whole genomes from these organisms would significantly enhance their discovery and genetic and functional charact...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq119
更新日期：2010-05-01 00:00:00
abstract：:Gene expression in Plasmodium falciparum is tightly regulated to ensure successful propagation of the parasite throughout its complex life cycle. The earliest transcriptomics studies in P. falciparum suggested a cascade of transcriptional activity over the course of the 48-hour intraerythrocytic developmental cycle (I...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx464
更新日期：2017-07-27 00:00:00
abstract：:Telomeres comprise the protective caps of natural chromosome ends and function in the suppression of DNA damage signaling and cellular senescence. Therefore, techniques used to determine telomere length are important in a number of studies, ranging from those investigating telomeric structure to effects on human disea...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt1315
更新日期：2014-02-01 00:00:00
abstract：:Nucleotide excision DNA repair is mechanistically conserved across all kingdoms of life. In prokaryotes, this multi-enzyme process requires six proteins: UvrA-D, DNA polymerase I and DNA ligase. To examine how UvrC locates the UvrB-DNA pre-incision complex at a site of damage, we have labeled UvrB and UvrC with differ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt177
更新日期：2013-05-01 00:00:00
