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：:We have sequenced the external transcribed spacer (ETS) of a ribosomal transcription unit from Xenopus laevis, together with sections of the preceding non-transcribed spacer. Our analysis was carried out on the same cloned transcription unit as that from which the internal transcribed spacers (ITS) were previously seq...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.7.2387
更新日期：1982-04-10 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：:The hammerhead self-cleaving motif occurs in a variety of RNAs that infect plants and consists of three non-conserved helices connected by a highly conserved central core. A variant hammerhead, called the extended hammerhead, is found in satellite 2 transcripts from a variety of caudate amphibians. The extended hammer...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.11.2189
更新日期：1997-06-01 00:00:00
abstract：:Here we analyze the effect of DNA folding on the performance of short primers and describe a simple technique for assessing hitherto uncertain values of thermodynamic parameters that determine the folding of single-stranded DNA into secondary structure. An 8mer with two degenerate positions is extended simultaneously ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.23.5525
更新日期：1998-12-01 00:00:00
abstract：:DNA helicases are required for virtually every aspect of DNA metabolism, including replication, repair, recombination and transcription. A comprehensive description of these essential biochemical processes requires detailed understanding of helicase mechanisms. These enzymes are ubiquitous, having been identified in v...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/gkl501
更新日期：2006-01-01 00:00:00
abstract：:A crucial component of the human mitochondrial DNA replisome is the ring-shaped helicase TWINKLE-a phage T7-gene 4-like protein expressed in the nucleus and localized in the human mitochondria. Our previous studies showed that despite being a helicase, TWINKLE has unique DNA annealing activity. At the time, the implic...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw098
更新日期：2016-05-19 00:00:00
abstract：:Alu insertions have contributed to >11% of the human genome and ∼30-35 Alu subfamilies remain actively mobile, yet the characterization of polymorphic Alu insertions from short-read data remains a challenge. We build on existing computational methods to combine Alu detection and de novo assembly of WGS data as a means...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1089
更新日期：2015-12-02 00:00:00
abstract：:Analysis of intergenic sequences for purposes such as the investigation of transcriptional signals or the identification of small RNA genes is frequently complicated by traditional biological database structures. Genome data is commonly treated as chromosome-length sequence records, detailed by gene calls demarcating ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg013
更新日期：2003-01-01 00:00:00
abstract：:It is common knowledge that conserved residues evolve slowly. We challenge generality of this central tenet of molecular biology by describing the fast evolution of a conserved nucleotide position that is located in the overlap of two open reading frames (ORFs) of polyomaviruses. The de novo ORF is expressed through e...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv378
更新日期：2015-05-26 00:00:00
abstract：:Eukaryotic genomes contain many endogenous retroviral sequences (ERVs). ERVs are often severely mutated, therefore difficult to detect. A platform independent (Java) program package, RetroTector (ReTe), was constructed. It has three basic modules: (i) detection of candidate long terminal repeats (LTRs), (ii) detection...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm515
更新日期：2007-01-01 00:00:00
abstract：:Identification of MHC-binding peptides is a prerequisite in rational design of T-cell based peptide vaccines. During the past decade a number of computational approaches have been introduced for the prediction of MHC-binding peptides, efficiently reducing the number of candidate binders that need to be experimentally ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl284
更新日期：2006-07-01 00:00:00
abstract：:The H19 lncRNA has been implicated in development and growth control and is associated with human genetic disorders and cancer. Acting as a molecular sponge, H19 inhibits microRNA (miRNA) let-7. Here we report that H19 is significantly decreased in muscle of human subjects with type-2 diabetes and insulin resistant ro...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1160
更新日期：2014-12-16 00:00:00
abstract：:Chloroplast DNA, isolated from a synchronized culture of Chlamydomonas reinhardii, was digested with restriction endonucleases and examined in the electron microscope. Restriction fragments containing displacement loops (D-loop) were photographed and measured to determine the position of replicated sequences in relati...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.9.3843
更新日期：1984-05-11 00:00:00
abstract：:We report the consensus sequence of members of a new dispersed middle-repetitive DNA family, MT, which is present in mouse and rat genomes. This family is shown to be as abundant as the described rodent B1 and B2 families. Hybridization experiments with radioactive single-stranded cDNAs from different tissues indicate...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.16.6403
更新日期：1986-08-26 00:00:00
abstract：:The synthesis of oligonucleotides (ODNs) containing 5-(N-aminohexyl)carbamoyl-2'-O-methyluridine (D) is described, and thermal stability and resistance to enzymatic hydrolysis of the ODNs are compared with ODNs containing 5-(N-aminohexyl)carbamoyl-2'-deoxyuridine (H). The ODNs containing D and the complementary RNA de...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg374
更新日期：2003-05-15 00:00:00
abstract：:Regulation of gene transcription in both prokaryotes and eukaryotes involves formation of various DNA-multiprotein complexes of higher order structure through communication between distant regions of DNA. The communication between distant DNA sites occurs by interaction between proteins bound to the sites by looping o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.4.873
更新日期：1997-02-15 00:00:00
abstract：:We have isolated and characterized a S. pombe promoter using a functional heterologous gene product assay. Random S. pombe genomic fragments were cloned upstream from the promoterless 'lacZ gene and tested in vivo for their efficiency to promote expression of the beta-galactosidase protein in the fission yeast. An eff...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.17.8603
更新日期：1988-09-12 00:00:00
abstract：:Phosphoprotein-binding domains (PPBDs) mediate many important cellular and molecular processes. Ten PPBDs have been known to exist in the human proteome, namely, 14-3-3, BRCT, C2, FHA, MH2, PBD, PTB, SH2, WD-40 and WW. PepCyber:P approximately PEP is a newly constructed database specialized in documenting human PPBD-c...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm854
更新日期：2008-01-01 00:00:00
abstract：:The National Center for Biotechnology Information (NCBI) provides a large suite of online resources for biological information and data, including the GenBank® nucleic acid sequence database and the PubMed database of citations and abstracts for published life science journals. The Entrez system provides search and re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx1095
更新日期：2018-01-04 00:00:00
abstract：:A mathematical model and a computer simulation were used to study PCR specificity. The model describes the occurrences of non-targeted PCR products formed through random primer-template interactions. The PCR simulation scans DNA sequence databases with primers pairs. According to the model prediction, PCR with complex...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.18.3538
更新日期：1996-09-15 00:00:00
abstract：:Three new proteins which selectively bind to UV-damaged DNA were identified and purified to near homogeneity from UV-irradiated Drosophila melanogaster embryos through several column chromatographies. These proteins, tentatively designated as D-DDB P1, P2 and P3, can be identified as different complex bands in a gel s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.14.2600
更新日期：1995-07-25 00:00:00
abstract：:Transcriptional repression and activation by nuclear receptors (NRs) are brought about by coregulator complexes. These complexes modify the chromatin environment of target genes and affect the activity of the basal transcription machinery. We have previously implicated the yeast ADA3 protein in transcriptional activat...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/30.11.2508
更新日期：2002-06-01 00:00:00
abstract：:Targeted delivery of antisense oligonucleotides (ASO) to hepatocytes via the asialoglycoprotein receptor (ASGR) has improved the potency of ASO drugs ∼30-fold in the clinic (1). In order to fully characterize the effect of GalNAc valency, oligonucleotide length, flexibility and chemical composition on ASGR binding, we...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx060
更新日期：2017-03-17 00:00:00
abstract：:Despite two decades of study, the full scope of RNAi in mammalian cells has remained obscure. Here we combine: (i) Knockout of argonaute (AGO) variants; (ii) RNA sequencing analysis of gene expression changes and (iii) Enhanced Crosslinking Immunoprecipitation Sequencing (eCLIP-seq) using anti-AGO2 antibody to identif...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkaa478
更新日期：2020-07-27 00:00:00
abstract：:Resolvase enzymes that cleave DNA four-way (Holliday) junctions are required for poxvirus replication, but clinically useful inhibitors have not been developed. Here, we report an assay for resolvase cleavage activity based on fluorescence polarization (FP) for high-throughput screening and mechanistic studies. Initia...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks325
更新日期：2012-09-01 00:00:00
abstract：:This article presents W-IQ-TREE, an intuitive and user-friendly web interface and server for IQ-TREE, an efficient phylogenetic software for maximum likelihood analysis. W-IQ-TREE supports multiple sequence types (DNA, protein, codon, binary and morphology) in common alignment formats and a wide range of evolutionary ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw256
更新日期：2016-07-08 00:00:00
abstract：T:Activator protein 1 (AP-1) is a transcription factor that recognizes two versions of a 7-base pair response element, either 5΄- GAG CA-3΄ or 5΄- GAG CA-3΄ (where M = 5-methylcytosine). These two elements share the feature that 5-methylcytosine and thymine both have a methyl group in the same position, 5-carbon of the...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx057
更新日期：2017-03-17 00:00:00
abstract：:IslandViewer (http://pathogenomics.sfu.ca/islandviewer) is a web-accessible application for the computational prediction and analysis of genomic islands (GIs) in bacterial and archaeal genomes. GIs are clusters of genes of probable horizontal origin and are of high interest because they disproportionately encode virul...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt394
更新日期：2013-07-01 00:00:00
abstract：:Period2 (Per2) is an essential component of the mammalian clock mechanism and robust circadian expression of Per2 is essential for the maintenance of circadian rhythms. Although recent studies have shown that the circadian E2 enhancer (a non-canonical E-box) accounts for most of the circadian transcriptional drive of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl868
更新日期：2007-01-01 00:00:00
abstract：:Most E2F-binding sites repress transcription through the recruitment of Retinoblastoma (RB) family members until the end of the G1 cell-cycle phase. Although the MYB promoter contains an E2F-binding site, its transcription is activated shortly after the exit from quiescence, before RB family members inactivation, by u...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx641
更新日期：2017-09-29 00:00:00
