Abstract：
:Microarrays are an effective tool for monitoring genome-wide gene expression levels. In current microarray analyses, the majority of genes on arrays are frequently eliminated for further analysis because the changes in their expression levels (ratios) are considered to be not significant. This strategy risks failure to discover whole sets of genes related to a quantitative trait of interest, which is generally controlled by several loci that make various contributions. Here, we describe a high-throughput gene discovery method based on correspondence analysis with a new index for expression ratios [arctan (1/ratio)] and three artificial marker genes. This method allows us to quickly analyze the whole microarray dataset and discover up-/down-regulated genes related to a trait of interest. We employed an example dataset to show the theoretical advantage of this method. We then used the method to identify 88 cancer-related genes from a published microarray data from patients with breast cancer. This method also allows us to predict the phenotype of a given sample from the gene expression profile. This method can be easily performed and the result is also visible in 3D viewing software that we have developed.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Yano K,Imai K,Shimizu A,Hanashita Tdoi
10.1093/nar/gkl058keywords:
subject
Has Abstractpub_date
2006-03-14 00:00:00pages
1532-9issue
5eissn
0305-1048issn
1362-4962pii
34/5/1532journal_volume
34pub_type
杂志文章abstract：:Efficient transcription from the human immunodeficiency virus (HIV) promoter depends on binding of the viral regulatory protein Tat to a cis-acting RNA regulatory element, TAR. Tat binds at a trinucleotide bulge located near the apex of the TAR stem-loop structure. An essential feature of Tat-TAR interaction is that t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/24.20.3974
更新日期：1996-10-15 00:00:00
abstract：:The allele frequency net database (http://www.allelefrequencies.net) is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. The extensive variability observed in genes and alleles related to the immune system response and its signi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq1128
更新日期：2011-01-01 00:00:00
abstract：:Arginyl-tRNA synthetase (ArgRS) catalyses AMP- and PPi-independent deacylation of Arg-tRNAArg in the presence of cysteine. A dipeptide, Arg-Cys, is a product of this deacylation reaction. Similar reaction with homocysteine yields Arg-Hcy. Arginine is a noncompetitive inhibitor of the cysteine-dependent deacylation whi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/23.22.4608
更新日期：1995-11-25 00:00:00
abstract：:Aspartic acid residues comprising the -D-(aa) n -Y-L-D-D- DNA polymerase active site triad of reverse transcriptase from the Saccharomyces cerevisiae long terminal repeat-retrotransposon Ty3 (Asp151, Asp213 and Asp214) were evaluated via site-directed mutagenesis. An Asp151-->Glu substitution showed a dramatic decreas...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki150
更新日期：2005-01-12 00:00:00
abstract：:Unwanted side effects of drugs are a burden on patients and a severe impediment in the development of new drugs. At the same time, adverse drug reactions (ADRs) recorded during clinical trials are an important source of human phenotypic data. It is therefore essential to combine data on drugs, targets and side effects...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1075
更新日期：2016-01-04 00:00:00
abstract：:Meiotic cells possess surveillance mechanisms that monitor critical events such as recombination and chromosome synapsis. Meiotic defects resulting from the absence of the synaptonemal complex component Zip1 activate a meiosis-specific checkpoint network resulting in delayed or arrested meiotic progression. Pch2 is an...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkw506
更新日期：2016-09-19 00:00:00
abstract：:The eukaryotic ribosomal protein S26e (rpS26e) lacking eubacterial counterparts is a key component of the ribosomal binding site of mRNA region 5' of the codon positioned at the exit site. Here, we determined the rpS26e oligopeptide neighboring mRNA on the human 80S ribosome using mRNA analogues bearing perfluoropheny...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkr1212
更新日期：2012-04-01 00:00:00
abstract：:Single-walled carbon nanotubes (SWNTs) have been considered as the leading candidate for nanodevice applications ranging from gene therapy and novel drug delivery to membrane separations. The miniaturization of DNA-nanotube devices for biological applications requires fully understanding DNA-nanotube interaction mecha...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl513
更新日期：2006-08-02 00:00:00
abstract：:There are a few algorithms designed to solve the problem of the optimal alignment of one sequence, the pattern, of length m, with another, longer sequence the text, of length n. These algorithms allow mismatches, deletions and insertions. Algorithms to date run in O(mn) time. Let us define an integer, k, which is the ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/14.1.31
更新日期：1986-01-10 00:00:00
abstract：:Transcriptomics (at the level of single cells, tissues and/or whole organisms) underpins many fields of biomedical science, from understanding the basic cellular function in model organisms, to the elucidation of the biological events that govern the development and progression of human diseases, and the exploration o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkq667
更新日期：2010-09-01 00:00:00
abstract：:Transcription of RNA from the beta-globin (major) gene in nuclei from induced mouse erythroleukemia cells terminates within the region between 700 to 2000 bases downstream from the poly(A) addition site, but not at particularly favored sites. In addition we present the first analysis of in vivo labeled RNA from a cell...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/12.22.8723
更新日期：1984-11-26 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：:Holliday junctions (four-way DNA junctions), formed during homologous recombination, are bound and resolved by junction-specific endonucleases to yield recombinant duplex DNA products. The junction-resolving enzymes are a structurally diverse class of proteins that nevertheless have many properties in common; in parti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/26.24.5609
更新日期：1998-12-15 00:00:00
abstract：:The paper presents measurements of the difference in the melting temperature of a colE1 DNA region when it is located inside the DNA helix and at its end. A direct comparison of calculations based on the rigorous theory of helix-coil transition with experimental data for .2 M Na+ (the conditions for fully reversible m...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/9.20.5469
更新日期：1981-10-24 00:00:00
abstract：:Humans have two nearly identical copies of the survival motor neuron (SMN ) gene, SMN1 and SMN2. Homozygous loss of SMN1 causes spinal muscular atrophy (SMA). SMN2 is unable to prevent the disease due to skipping of exon 7. Using a systematic approach of in vivo selection, we have previously demonstrated that a weak 5...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkl1050
更新日期：2007-01-01 00:00:00
abstract：:Mutations in mammalian and Drosophila Hel308 and PolQ paralogues cause genome instability but their helicase functions are mysterious. By in vivo and in vitro analysis, we show that Hel308 from archaea (Hel308a) may act at stalled replication forks. Introducing hel308a into Escherichia coli dnaE strains that condition...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gki685
更新日期：2005-06-30 00:00:00
abstract：:Signaling pathways constitute a valuable source of information that allows interpreting the way in which alterations in gene activities affect to particular cell functionalities. There are web tools available that allow viewing and editing pathways, as well as representing experimental data on them. However, few metho...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt451
更新日期：2013-07-01 00:00:00
abstract：:Chromatin footprinting in Drosophila tissue culture cells has detected the binding of a non-histone protein at +8 of the distal Adh RNA start site, on a 10-bp direct repeat motif abutting a nucleosome positioned over the inactive Adh distal promoter. Alternatively the active promoter is bound by a transcription initia...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.17.4481
更新日期：1992-09-11 00:00:00
abstract：:The database of Clusters of Orthologous Groups of proteins (COGs), which represents an attempt on a phylogenetic classification of the proteins encoded in complete genomes, currently consists of 2791 COGs including 45 350 proteins from 30 genomes of bacteria, archaea and the yeast Saccharomyces cerevisiae (http://www....
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.1.22
更新日期：2001-01-01 00:00:00
abstract：:LNA oligonucleotides constitute a class of bicyclic RNA analogues having an exceptionally high affinity for their complementary DNA and RNA target molecules. We here report a novel method for highly efficient isolation of intact poly(A)+ RNA using an LNA-substituted oligo(dT) affinity ligand, based on the increased af...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnh056
更新日期：2004-04-19 00:00:00
abstract：:Despite the large number of noncoding RNAs in human genome and their roles in many diseases include cancer, we know very little about them due to lack of structural clues. The centerpiece of the structural clues is the full RNA base-pairing structure of secondary and tertiary contacts that can be precisely obtained on...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz1192
更新日期：2020-02-20 00:00:00
abstract：:The goal of the present study is to identify genes that respond to iron availability. Suppression subtraction hybridization (SSH) was used to generate cDNA libraries from iron loaded and control human astrocytoma cells (SW1088). The cDNA libraries were screened with antisense cDNA probes obtained from mRNA isolated fr...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/28.8.1802
更新日期：2000-04-15 00:00:00
abstract：:Gene set enrichment testing can enhance the biological interpretation of ChIP-seq data. Here, we develop a method, ChIP-Enrich, for this analysis which empirically adjusts for gene locus length (the length of the gene body and its surrounding non-coding sequence). Adjustment for gene locus length is necessary because ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku463
更新日期：2014-07-01 00:00:00
abstract：:In kinetoplastid protozoa, mitochondrial (mt) mRNAs are post-transcriptionally edited by insertion and deletion of uridylate residues, the information being provided by guide (g)RNAs. Currently popular mechanisms for the editing process envisage a series of consecutive 'cut-and-paste' reactions, carried out by a compl...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.14.2950
更新日期：2001-07-15 00:00:00
abstract：:The strand displacement activity of DNA polymerase δ is strongly stimulated by its interaction with proliferating cell nuclear antigen (PCNA). However, inactivation of the 3'-5' exonuclease activity is sufficient to allow the polymerase to carry out strand displacement even in the absence of PCNA. We have examined in ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv260
更新日期：2015-04-30 00:00:00
abstract：:We describe the structure (3840 bp) of a novel Euglena gracilis chloroplast ribosomal protein operon that encodes the five genes rpl16-rpl14-rpl5-rps8-rpl36. The gene organization resembles the spc and the 3'-end of the S10 ribosomal protein operons of E. coli. The rpl5 is a new chloroplast gene not previously reporte...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/17.19.7591
更新日期：1989-10-11 00:00:00
abstract：:The family of ten-eleven translocation (Tet) dioxygenases is widely distributed across the eukaryotic tree of life, from mammals to the amoeboflagellate Naegleria gruberi. Like mammalian Tet proteins, the Naegleria Tet-like protein, NgTet1, acts on 5-methylcytosine (5mC) and generates 5-hydroxymethylcytosine (5hmC), 5...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv870
更新日期：2015-12-15 00:00:00
abstract：:Type IV effectors (T4Es) are proteins produced by pathogenic bacteria to manipulate host cell gene expression and processes, divert the cell machinery for their own profit and circumvent the immune responses. T4Es have been characterized for some bacteria but many remain to be discovered. To help biologists identify p...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkt718
更新日期：2013-11-01 00:00:00
abstract：:Type II restriction endonucleases Bam HI and Eco RI were covalently coupled to Sepharose. These insolubilized enzymes generated fragment patterns for several viral DNAs identical to those produced by the respective free enzymes. Conditions for optimal activity were similar for both bound and unbound forms of the enzym...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/5.3.679
更新日期：1978-03-01 00:00:00
abstract：:The repeating nucleotide sequence of 68 base pairs in the mtDNA from an ethidium-induced cytoplasmic petite mutant of yeast has been determined. For sequence analysis specifically primed and terminated RNA copies, obtained by in vitro transcription of the separated strands, were use. The sequence consists of 66 consec...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/4.7.2369
更新日期：1977-07-01 00:00:00
