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 defines five quality scores for each spot to record irregularities in spot intensity, size and background noise levels. A composite score q(com) is defined based on these individual scores to give an overall assessment of spot quality. Using q(com) we demonstrate that the inherent variability in intensity ratio measurements is closely correlated with spot quality, namely spots with higher quality give less variable measurements and vice versa. In addition, gauging data by q(com) can improve data reliability dramatically and efficiently. We further show that the variability in ratio measurements drops exponentially with increasing q(com) and, for the majority of spots at the high quality end, this improvement is mainly due to an improvement in correlation between the two dyes. Based on these studies, we discuss the potential of quantitative quality control for microarray data and the possibility of filtering and normalizing microarray data using a quality metrics-dependent scheme.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Wang X,Ghosh S,Guo SWdoi
10.1093/nar/29.15.e75keywords:
subject
Has Abstractpub_date
2001-08-01 00:00:00pages
E75-5issue
15eissn
0305-1048issn
1362-4962journal_volume
29pub_type
杂志文章abstract::The chemical reactivity of matched T and C bases to osmium tetroxide and hydroxylamine near mismatched and unmatched bases in a heteroduplex between two strands of DNA with multiple differences was examined. Data was available for matched bases one or two positions away from 24 mismatches. Reactive bases were found ne...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.11.4223
更新日期:1989-06-12 00:00:00
abstract::Bacterial small RNAs (sRNAs) are a heterogeneous group of post-transcriptional regulators that often act at the heart of large networks. Hundreds of sRNAs have been discovered by genome-wide screens and most of these sRNAs exert their functions by base-pairing with target mRNAs. However, studies addressing the molecul...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky765
更新日期:2018-11-16 00:00:00
abstract::Arylsulfatase, produced by Chlamydomonas reinhardtii during sulfur-limited growth, is secreted into the periplasmic space and is readily assayed using a chromogenic substrate. To assess the usefulness of the gene encoding arylsulfatase (ars) as a reporter gene in C. reinhardtii, we have fused the promoter region of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.12.2959
更新日期:1992-06-25 00:00:00
abstract::H3K4me3 is a histone modification that accumulates at the transcription-start site (TSS) of active genes and is known to be important for transcription activation. The way in which H3K4me3 is regulated at TSS and the actual molecular basis of its contribution to transcription remain largely unanswered. To address thes...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks773
更新日期:2012-10-01 00:00:00
abstract::Over the past 10 years, fluorescent end-labeling of DNA fragments has evolved into the preferred method of DNA detection for a wide variety of applications, including DNA sequencing and PCR fragment analysis. One of the advantages inherent in fluorescent detection methods is the ability to perform multi-color analyses...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.11.2797
更新日期:1998-06-01 00:00:00
abstract::We have studied the role of the C-terminal domain of the alpha subunit (alphaCTD) of Escherichia coli RNA polymerase during transcription initiation at promoters lacking an UP-element. The temperature requirement for open complex formation was used as an indication of the kinetics of this process. We have previously s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.9.2051
更新日期:1999-05-01 00:00:00
abstract::Extracts of the human glioma cell line A1235 (lacking O(6)-methylguanine-DNA methyltransferase) are known to restore a G:T mismatch to a normal G:C pair in a G:T-containing model (45 bp) DNA substrate. Herein we demonstrate that substitution of G:T with O(6)-methylguanine:T (m6G:T) results in extract-induced intra-str...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.11.2409
更新日期:2001-06-01 00:00:00
abstract::The thyroid hormone receptor alpha (THRA or c-erbA-1) gene belongs to a family of genes which encode nuclear receptors for various hydrophobic ligands such as steroids, vitamin D, retinoic acid and thyroid hormones. These receptors are composed of several domains important for hormone-binding, DNA-binding, dimerizatio...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.5.1105
更新日期:1991-03-11 00:00:00
abstract::Recent research hints at an underappreciated complexity in pre-miRNA processing and regulation. Global profiling of pre-miRNA and its potential to increase understanding of the pre-miRNA landscape is impeded by overlap with highly expressed classes of other non coding (nc) RNA. Here, we present a data set excluding th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr903
更新日期:2012-02-01 00:00:00
abstract::A fluoride-cleavable phosphoramidite for biotinylation was designed, synthesized and coupled efficiently to the 5'-end of DNA on an automatic synthesizer. The diisopropylsilyl acetal functionality was used to link the biotin moiety through a tertiary hydroxide group to the 5'-end of DNA. This linkage proved to be comp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg130
更新日期:2003-01-15 00:00:00
abstract::Autosomal dominant and/or recessive progressive external ophthalmoplegia (ad/arPEO) is associated with mtDNA mutagenesis. It can be caused by mutations in three nuclear genes, encoding the adenine nucleotide translocator 1, the mitochondrial helicase Twinkle or DNA polymerase gamma (POLG). How mutations in these genes...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh634
更新日期:2004-06-04 00:00:00
abstract::Plasmids p749, p106, and p150 contain cDNA inserts complementary to rat skeletal muscle actin mRNA. Nucleotide sequence analysis indicates the following sequence relationships: p749 specifies codons 171 to 360; p150 specifies codons 357 to 374 together with 120 nucleotides of the 3'-non-translated region; p106 specifi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.3.579
更新日期:1981-02-11 00:00:00
abstract::Studies involving ribozyme-directed inactivation of targeted RNA molecules have met with mixed success, making clear the importance of methods to measure and optimize ribozyme activity within cells. The interpretation of biochemical assays for determining ribozyme activity in the cellular environment have been complic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.15.3494
更新日期:1998-08-01 00:00:00
abstract::Dlx2, Lymphoid Enhancer Factor (Lef-1) and Msx2 transcription factors are required for several developmental processes. To understand the control of gene expression by these factors, chromatin immunoprecipitation (ChIP) assays identified Msx2 as a downstream target of Dlx2 and Lef-1. Dlx2 activates the Msx2 promoter i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl689
更新日期:2006-01-01 00:00:00
abstract::The signal recognition particle database (SRPDB) is located at the University of Texas Health Science Center at Tyler and includes tabulations of SRP RNA, SRP protein and SRP receptor sequences. The sequences are annotated with links to the primary databases. They are ordered alphabetically or phylogenetically and are...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.1.169
更新日期:1999-01-01 00:00:00
abstract::We have carried out a survey of potential quadruplex structure sequences (PQSS), which occur in the immediate upstream region (500 bp) of human genes. By examining the number and distribution of these we have established that there is a clear link between them and the occurrence of the SP1-binding element 'GGGCGG', su...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn078
更新日期:2008-05-01 00:00:00
abstract::NELF and DSIF act together to inhibit transcription elongation in vitro, and are implicated in causing promoter proximal pausing on the hsp70 gene in Drosophila. Here, further characterization of Drosophila NELF is provided. Drosophila NELF has four subunits similar to subunits of human NELF. The amino acid sequences ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki274
更新日期:2005-03-01 00:00:00
abstract::RNA-based therapeutics, i.e. the utilization of synthetic RNA molecules to alter cellular functions, have the potential to address targets which are currently out of scope for traditional drug design pipelines. This potential however hinges on the ability to selectively deliver and internalize therapeutic RNAs into ce...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky577
更新日期:2018-09-19 00:00:00
abstract::Studying the intricate folding of rRNA within the ribosome remains a complex problem. Phenanthroline-Cu(II) complexes cleave phosphodiester bonds in rRNA in specific regions, apparently especially where the rRNA structure is constrained in some fashion. We have introduced phenanthroline-copper complexes into 50S Esche...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.8.1906
更新日期:1999-04-15 00:00:00
abstract::Understanding the evolutionary and genomic mechanisms responsible for turning the soil-derived saprophytic mycobacteria into lethal intracellular pathogens is a critical step towards the development of strategies for the control of mycobacterial diseases. In this context, Mycobacterium indicus pranii (MIP) is of speci...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks793
更新日期:2012-11-01 00:00:00
abstract::Due to the importance of protein phosphorylation in cellular control, many researches are undertaken to predict the kinase-specific phosphorylation sites. Referred to our previous work, KinasePhos 1.0, incorporated profile hidden Markov model (HMM) with flanking residues of the kinase-specific phosphorylation sites. H...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm322
更新日期:2007-07-01 00:00:00
abstract::Experimental evidence indicates that about 60% of miRNA-binding activity does not follow the canonical rule about the seed matching between miRNA and target mRNAs, but rather a non-canonical miRNA targeting activity outside the seed or with a seed-like motifs. Here, we propose a new unbiased method to identify canonic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx007
更新日期:2017-05-19 00:00:00
abstract::The results of differential expression analyses provide scientists with hundreds to thousands of differentially expressed genes that need to be interpreted in light of the biology of the specific system under study. This requires mapping the genes to functional classifications that can be, for example, the KEGG pathwa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt516
更新日期:2013-07-01 00:00:00
abstract::Linear motifs are short, evolutionarily plastic components of regulatory proteins and provide low-affinity interaction interfaces. These compact modules play central roles in mediating every aspect of the regulatory functionality of the cell. They are particularly prominent in mediating cell signaling, controlling pro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr1064
更新日期:2012-01-01 00:00:00
abstract::We describe a novel 3'-OH unblocked reversible terminator with the potential to improve accuracy and read-lengths in next-generation sequencing (NGS) technologies. This terminator is based on 5-hydroxymethyl-2'-deoxyuridine triphosphate (HOMedUTP), a hypermodified nucleotide found naturally in the genomes of numerous ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq1293
更新日期:2011-03-01 00:00:00
abstract::Systematic structure probing experiments (e.g. SHAPE) of RNA mutants such as the mutate-and-map (MaM) protocol give us a direct access into the genetic robustness of ncRNA structures. Comparative studies of homologous sequences provide a distinct, yet complementary, approach to analyze structural and functional proper...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw217
更新日期:2016-06-20 00:00:00
abstract::The 5' portions and flanking sequences of genes encoding types 1, 12, 24, and 6 M proteins were compared. Although the DNA sequences encoding the amino-termini of the mature M proteins had no obvious similarity, upstream sequences, and those encoding the signal peptides (leader sequences) of the four M protein genes h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.10.4667
更新日期:1988-05-25 00:00:00
abstract::Functional genomic elements are marked by characteristic DNA and histone modification signatures. How combinatorial chromatin modification states are recognized by epigenetic reader proteins and how this is linked to their biological function is largely unknown. Here we provide a detailed molecular analysis of chromat...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw979
更新日期:2017-02-17 00:00:00
abstract::Using a genetic selection for suppressors of a UGA nonsense mutation in trpA, we have isolated a G to A transition mutation at position 1491 in the decoding region of 16S rRNA. This suppressor displayed no codon specificity, suppressing UGA, UAG and UAA nonsense mutations and +1 and -1 frameshift mutations in lacZ. Su...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.21.4234
更新日期:1995-11-11 00:00:00
abstract::Several cDNA clones were isolated from cDNA libraries constructed with mRNA longer than 28S RNA from the murine cell line PYS-2/12. The plasmids have inserts containing 1-1.2 kb of the ribosomal 5' external transcribed spacer followed by nearly 700 nt of sequence for 18S rRNA and ending with a B2 element (retroposon)....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.4.671
更新日期:1992-02-25 00:00:00