Abstract：
:Exome sequencing strategy is promising for finding novel mutations of human monogenic disorders. However, pinpointing the casual mutation in a small number of samples is still a big challenge. Here, we propose a three-level filtration and prioritization framework to identify the casual mutation(s) in exome sequencing studies. This efficient and comprehensive framework successfully narrowed down whole exome variants to very small numbers of candidate variants in the proof-of-concept examples. The proposed framework, implemented in a user-friendly software package, named KGGSeq (http://statgenpro.psychiatry.hku.hk/kggseq), will play a very useful role in exome sequencing-based discovery of human Mendelian disease genes.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Li MX,Gui HS,Kwan JS,Bao SY,Sham PCdoi
10.1093/nar/gkr1257subject
Has Abstractpub_date
2012-04-01 00:00:00pages
e53issue
7eissn
0305-1048issn
1362-4962pii
gkr1257journal_volume
40pub_type
杂志文章abstract：:In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides analysis and retrieval resources for the data in GenBank and other biological data available through NCBI's web site. NCBI resources include Entrez, the Entrez Programming Utiliti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm1000
更新日期：2008-01-01 00:00:00
abstract：:Our web server, PIZSA (http://cospi.iiserpune.ac.in/pizsa), assesses the likelihood of protein-protein interactions by assigning a Z Score computed from interface residue contacts. Our score takes into account the optimal number of atoms that mediate the interaction between pairs of residues and whether these contacts...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz368
更新日期：2019-07-02 00:00:00
abstract：:A sixty base pair DNA duplex containing the nucleotide sequence of the bacteriophage T5 early (T5P25) promoter has been constructed using a combination of chemical synthesis and enzymatic methods. Subsequent to cloning into pBR322, the promoter has been demonstrated to be biologically active being capable of directing...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/11.17.5921
更新日期：1983-09-10 00:00:00
abstract：:We have adapted a method for making libraries of mutations in any specific gene for use in the fission yeast Schizosaccharomyces pombe . This elegant and simple method consists of PCR amplification of the gene of interest, followed by co-transformation of fission yeast with the PCR fragment and a linearized plasmid ve...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.20.4783
更新日期：1998-10-15 00:00:00
abstract：:Expansions of (GAA)n repeats within the first intron of the frataxin gene reduce its expression, resulting in a hereditary neurodegenerative disorder, Friedreich's ataxia. While it is generally believed that expanded (GAA)n repeats block transcription elongation, fine mechanisms responsible for gene repression are not...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl1140
更新日期：2007-01-01 00:00:00
abstract：:As the formation of ribonucleoprotein complexes is a major mechanism of angiotensin II type 1 receptor (AT1R) regulation, we sought to identify novel AT1R mRNA binding proteins. By affinity purification and mass spectroscopy, we identified TIA-1. This interaction was confirmed by colocalization of AT1R mRNA and TIA-1 ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1368
更新日期：2016-04-20 00:00:00
abstract：:The transmission of genetic information relies on Watson-Crick base pairing between nucleoside phosphates and template bases in template-primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequenc...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku314
更新日期：2014-06-01 00:00:00
abstract：:A highly polymorphic locus associated with the variable tandem repetition of a 35 bp consensus sequence was mapped to chromosome 10, band q26. Examination of leukocyte DNA from a cancer patient revealed the twenty-fold amplification of one allelic fragment of this locus, while the other allelic fragment demonstrated a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.20.7929
更新日期：1986-10-24 00:00:00
abstract：:Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. In addition to classical tree viewer functions, iTOL offers many novel ways of annotating trees with various additional data. Current versi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr201
更新日期：2011-07-01 00:00:00
abstract：:Conserved in a variety of evolutionarily divergent plant species, LOB DOMAIN (LBD) genes define a large, plant-specific family of largely unknown function. LBD genes have been implicated in a variety of developmental processes in plants, although to date, relatively few members have been assigned functions. LBD protei...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm775
更新日期：2007-01-01 00:00:00
abstract：:We attempted to use the polymerase chain reaction (PCR) to monitor in vitro recombination in a plasmid containing directly repeated sequences. Some of the plasmid preparations which had not been exposed to recombination conditions were however found to behave in the PCR test as if they had undergone homologous recombi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.9.2423
更新日期：1991-05-11 00:00:00
abstract：:Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-bas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1165
更新日期：2015-01-01 00:00:00
abstract：:The Human Genome Project has facilitated the sequencing of many species, yet the current Sanger method is too expensive, labor intensive and time consuming to accomplish medical resequencing of human genomes en masse. Of the 'next-generation' technologies, cyclic reversible termination (CRT) is a promising method with...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm689
更新日期：2007-01-01 00:00:00
abstract：:The RNA-Seq technology has revolutionized transcriptome characterization not only by accurately quantifying gene expression, but also by the identification of novel transcripts like chimeric fusion transcripts. The 'fusion' or 'chimeric' transcripts have improved the diagnosis and prognosis of several tumors, and have...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkx315
更新日期：2017-07-27 00:00:00
abstract：:Large differences in plant genome sizes are mainly due to numerous events of insertions or deletions (indels). The balance between these events determines the evolutionary direction of genome changes. To address the question of what phenomena trigger these alterations, we compared the genomic sequences of two Arabidop...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp183
更新日期：2009-06-01 00:00:00
abstract：:We have determined the DNA sequence surrounding the transcription terminator following rpoC, the gene that codes for the beta' subunit of RNA polymerase in E. coli K12. The 2044 bp sequence obtained contains the distal 335 codons of rpoC followed by a 212 bp non-coding region and a second open reading frame (ORFa) of ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.24.6827
更新日期：1981-12-21 00:00:00
abstract：:The transcriptional regulator Spx plays a key role in maintaining the redox homeostasis of Bacillus subtilis cells exposed to disulfide stress. Defects in Spx were previously shown to lead to differential expression of numerous genes but direct and indirect regulatory effects could not be distinguished. Here we identi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks755
更新日期：2012-10-01 00:00:00
abstract：:Ribotoxins are potent inhibitors of protein biosynthesis and inactivate ribosomes from a variety of organisms. The ribotoxin alpha-sarcin cleaves the large 23S ribosomal RNA (rRNA) at the universally conserved sarcin-ricin loop (SRL) leading to complete inactivation of the ribosome and cellular death. The SRL interact...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq151
更新日期：2010-07-01 00:00:00
abstract：:Stabilization of stalled replication forks prevents excessive fork reversal or degradation, which can undermine genome integrity. The WRN protein is unique among the other human RecQ family members to possess exonuclease activity. However, the biological role of the WRN exonuclease is poorly defined. Recently, the WRN...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz431
更新日期：2019-07-26 00:00:00
abstract：:Photoalkylation reactions with 2-propanol, initiated with di-tert-butyl peroxide, of a variety of purine and pyrimidine mononucleotides and dinucleoside monophosphates lead to the substitution of an alpha-hydroxyisopropyl group for the H-8 atom of adenosine and the addition of the alcohol across the 5,6-double bond of...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/3.7.1715
更新日期：1976-07-01 00:00:00
abstract：:Nucleic acids possess the unique property of being enzymatically amplifiable, and have therefore been a popular choice for the combinatorial selection of functional sequences, such as aptamers or ribozymes. However, amplification typically requires known sequence segments that serve as primer binding sites, which can ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks004
更新日期：2012-05-01 00:00:00
abstract：:Procollagen alpha 2 (I) mRNA can be induced congruent to 6-fold in primary avian tendon (PAT) cells on addition of ascorbate to the culture medium. Previously, we have shown that the induction is linear after a 12 h lag and requires a total of 60-72 h to achieve maximum levels. We have now investigated in more detail ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.5.2569
更新日期：1984-03-12 00:00:00
abstract：:We investigated the effects of the antiviral agent distamycin A and of a distamycin derivative (FCE 24517) which possesses antineoplastic activity on the binding of some regulatory proteins to DNA. Both compounds inhibited the binding to DNA of the ubiquitous octamer binding factor OTF 1 and of the erythroid specific ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.3.1051
更新日期：1989-02-11 00:00:00
abstract：:More than 200 assembly factors (AFs) are required for the production of ribosomes in yeast. The stepwise association and dissociation of these AFs with the pre-ribosomal subunits occurs in a hierarchical manner to ensure correct maturation of the pre-rRNAs and assembly of the ribosomal proteins. Although decades of re...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz1079
更新日期：2020-01-10 00:00:00
abstract：:MicroRNAs (miRNAs) are short, non-protein coding RNAs that direct the widespread phenomenon of post-transcriptional regulation of metazoan genes. The mature approximately 22-nt long RNA molecules are processed from genome-encoded stem-loop structured precursor genes. Hundreds of such genes have been experimentally val...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn707
更新日期：2009-01-01 00:00:00
abstract：:An enzyme capable of liberating functional tRNA(Lys) from Escherichia coli diacetyl-lysyl-tRNA(Lys) was purified from the archae Sulfolobus solfataricus. Contrasting with the specificity of peptidyl- tRNA hydrolase (PTH) from E.coli, the S.solfataricus enzyme readily accepts E.coli formyl-methionyl-tRNA(fMet) as a sub...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg428
更新日期：2003-06-15 00:00:00
abstract：:This paper describes the sequence of 257 nucleotides from the 3' end of RNA 2 of barley stripe mosaic virus ( BSMV , strain Argentina Mild) including an internal oligo (A) tract localized at a distance of 236 nucleotides from the 3' end, and the 3' terminal tRNA-like structure accepting tyrosine. This sequence is show...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.9.4001
更新日期：1984-05-11 00:00:00
abstract：:The APOBEC3 proteins are unique to mammals. Many inhibit retrovirus infection through a cDNA cytosine deamination mechanism. HIV-1 neutralizes this host defense through Vif, which triggers APOBEC3 ubiquitination and degradation. Here, we report an APOBEC3F-like, double deaminase domain protein from three artiodactyls:...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl721
更新日期：2006-01-01 00:00:00
abstract：:From a library of nucleic acid molecules, which are randomized in parts of their sequence, unique sequence variants can be selected for specific properties. The planning of such an in vitro selection experiment requires some consideration regarding how much DNA template or RNA transcript should be used initially. The ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.17.3437
更新日期：1996-09-01 00:00:00
abstract：:We determined the structure around the gap region between 28S alpha and 28S beta rRNA of Bombyx mori, a lepidopteran insect, to know the introduction mechanism of the hidden break, an interruption of the phosphodiester bond specific to the 28S rRNA of protostomes. Sequence analysis and S1 nuclease mapping suggested th...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.16.6393
更新日期：1986-08-26 00:00:00
