Abstract:
:Exon arrays are regularly used to analyze differential splicing events. GeneChip Gene 1.0 ST Arrays (gene arrays) manufactured by Affymetrix, Inc. are primarily used to determine expression levels of transcripts, although their basic design is rather similar to GeneChip Exon 1.0 ST Arrays (exon arrays). Here, we show that the newly developed Gene Array Analyzer (GAA), which evolved from our previously published Exon Array Analyzer (EAA), enables economic and user-friendly analysis of alternative splicing events using gene arrays. To demonstrate the applicability of GAA, we profiled alternative splicing events during embryonic heart development. In addition, we found that numerous developmental splicing events are also activated under pathological conditions. We reason that the usage of GAA considerably expands the analysis of gene expression based on gene arrays and supplies an additional level of information without further costs and with only little effort.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Gellert P,Teranishi M,Jenniches K,De Gaspari P,John D,Kreymborg Kg,Braun T,Uchida Sdoi
10.1093/nar/gkr1110subject
Has Abstractpub_date
2012-03-01 00:00:00pages
2414-25issue
6eissn
0305-1048issn
1362-4962pii
gkr1110journal_volume
40pub_type
杂志文章abstract::We have recently developed a novel method for the affinity purification of the complete suite of translating mRNA from genetically labeled cell populations. This method permits comprehensive quantitative comparisons of the genes employed by each specific cell type. We provide a detailed description of tools for analys...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq130
更新日期:2010-07-01 00:00:00
abstract::Three clones of non-repetitive sequences and six clones containing repetitive sequences were obtained from micronuclear DNA of Tetrahymena thermophila. All the non-repetitive and three repetitive sequences had the same organization in micro- and macronuclear DNAs as revealed by blot hybridization. On the other hand, t...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.14.4279
更新日期:1982-07-24 00:00:00
abstract::Translesion synthesis (TLS) employs low fidelity polymerases to replicate past damaged DNA in a potentially error-prone process. Regulatory mechanisms that prevent TLS-associated mutagenesis are unknown; however, our recent studies suggest that the PCNA-binding protein Spartan plays a role in suppression of damage-ind...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1267
更新日期:2013-02-01 00:00:00
abstract::A novel program suite was implemented for the functional interpretation of high-throughput gene expression data based on the identification of Gene Ontology (GO) nodes. The focus of the analysis lies on the interpretation of microarray data from prokaryotes. The three well established statistical methods of the thresh...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl329
更新日期:2006-07-01 00:00:00
abstract::Slime mold, plant and insect dihydropyrimidine amidohydrolases (DHPases, EC 3.5.2.2), which catalyze the second step of pyrimidine and several anti-cancer drug degradations, were cloned and shown to functionally replace a defective DHPase enzyme in the yeast Saccharomyces kluyveri. The yeast and slime mold DHPases wer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg258
更新日期:2003-03-15 00:00:00
abstract::The proportion of cytosines methylated in the DNA of nucleosome oligomers and of core particles appears indistinguishable from that of total nuclear DNA from CHO cells. However the DNA in nucleoprotein which is initially released from nuclei by treatment with very low levels of micrococcal nuclease and the first 10% o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/4.9.3097
更新日期:1977-09-01 00:00:00
abstract::Three novel DNA-binding proteins with apparent molecular masses of 7, 10 and 30 kDa have been isolated from the hyperthermophilic methanogen Methanopyrus kandleri. The proteins were identified using a blot overlay assay that was modified to emulate the high ionic strength intracellular environment of M.kandleri protei...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.3.685
更新日期:2002-02-01 00:00:00
abstract::Gene duplications are a major source of evolutionary innovations. Understanding the functional divergence of duplicates and their role in genetic robustness is an important challenge in biology. Previously, analyses of genetic robustness were primarily focused on duplicates essentiality and epistasis in several labora...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt1200
更新日期:2014-02-01 00:00:00
abstract::As opposed to the vast majority of prokaryotic repressors, the immunity repressor of temperate Escherichia coli phage P2 (C) recognizes non-palindromic direct repeats of DNA rather than inverted repeats. We have determined the crystal structure of P2 C at 1.8 Å. This constitutes the first structure solved from the fam...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq626
更新日期:2010-11-01 00:00:00
abstract::In eukaryotes, DNA is packaged into a basic unit, the nucleosome which consists of 147 bp of DNA wrapped around a histone octamer composed of two copies each of the histones H2A, H2B, H3 and H4. Nucleosome structures are diverse not only by histone variants, histone modifications, histone composition but also through ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv276
更新日期:2015-04-30 00:00:00
abstract::Oligonucleotide-directed mutagenesis was used to introduce an A to C transversion at position 523 in the 16S ribosomal RNA gene of Escherichia coli rrnB operon cloned in plasmid pKK3535. E. coli cells transformed with the mutated plasmid were resistant to streptomycin. The mutated ribosomes isolated from these cells w...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.20.9631
更新日期:1988-10-25 00:00:00
abstract::Interactions between proteins, drugs, water and B-DNA minor groove have been analyzed in crystal structures of 60 protein-DNA and 14 drug-DNA complexes. It was found that only purine N3, pyrimidine O2, guanine N2 and deoxyribose O4' are involved in the interactions, and that contacts to N3 and O2 are most frequent and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.5.1182
更新日期:2002-03-01 00:00:00
abstract::With the improved secreted protein prediction approach and comprehensive data sources, including Swiss-Prot, TrEMBL, RefSeq, Ensembl and CBI-Gene, we have constructed secretomes of human, mouse and rat, with a total of 18 152 secreted proteins. All the entries are ranked according to the prediction confidence. They we...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki093
更新日期:2005-01-01 00:00:00
abstract::Genomic Denaturing Gradient Gel Electrophoresis (gDGGE) provides an alternative to the standard method of restriction fragment length polymorphism (RFLP) analysis for identifying polymorphic sequence variation in genomic DNA. For gDGGE, genomic DNA is cleaved by restriction enzymes, separated in a polyacrylamide gel c...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.7.1475
更新日期:1991-04-11 00:00:00
abstract::Hammerhead ribozymes were transcribed from a dsDNA template containing four random nucleotides between stems II and III, which replace the naturally occurring GAA nucleotides. In vitro selection was used to select hammerhead ribozymes capable of in cis cleavage using denaturing polyacrylamide gels for the isolation of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.22.4401
更新日期:1996-11-15 00:00:00
abstract::The effect of different levels of mercury substitution on the rate and extent of hybridisation of globin mRNA with a complementary DNA (cDNA) copy has been investigated. It was found that mercuration significantly reduces both the rate of hybridisation and the extent of the reaction, but that these effects are abolish...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/7.8.2357
更新日期:1979-12-20 00:00:00
abstract::The precursor to the Euglena light harvesting chlorophyll a/b binding protein of photosystem II (LHCPII) is a polyprotein containing multiple copies of LHCPII covalently joined by a decapeptide linker. cDNA and genomic clones encoding the 5' and 3' end of a 6.6 kb LHCPII mRNA were sequenced. A 3.1 kb genomic region en...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.25.5737
更新日期:1994-12-25 00:00:00
abstract::A phosphotriester solid phase method on a polyamide support has been used to prepare oligodeoxyribonucleotides up to 12 units long. Compared to solid phase phosphodiester synthesis the new methodology is quicker, more flexible and gives 10-60-fold better overall yields. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.5.1081
更新日期:1980-03-11 00:00:00
abstract::Cellular membranes feature dynamic submicrometer-scale lateral domains termed lipid rafts, membrane rafts or glycosphingolipid-enriched microdomains (GEM). Numerous proteomics studies have been conducted on the lipid raft proteome, however, interpretation of individual studies is limited by potential undefined contami...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky948
更新日期:2019-01-08 00:00:00
abstract::Analysis of the human VK (ref. 2) gene locus led to the detection of a new sequence family (L sequences). Its copy number is in the range of 10(2). The L sequences, which are about 500 bp long, are found as part of the 3' flanking regions of a clustered set of human VKI genes but they occur also separate from the gene...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.13.5265
更新日期:1984-07-11 00:00:00
abstract::The history and mechanism of molecular evolution in DNA have been greatly elucidated by contributions from genetics, probability theory and bioinformatics--indeed, mathematical developments such as Kimura's neutral theory, Kingman's coalescent theory and efficient software such as BLAST, ClustalW, Phylip, etc., provid...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp477
更新日期:2009-07-01 00:00:00
abstract::Current knowledge of parameters affecting RNA stability is very restricted in plants. Here we investigated factors which might contribute to the stability of a particular plant messenger RNA. To this end, insertion and deletion mutants were made in two different exons and an intron of the transcribed region of a well ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.10.2917
更新日期:1990-05-25 00:00:00
abstract::Synthesis of HIV GagPol involves a proportion of ribosomes translating a U6A shift site at the distal end of the gag gene performing a programmed -1 ribosomal frameshift event to enter the overlapping pol gene. In vitro studies here show that at the same shift motif HIV reverse transcriptase generates -1 and +1 indels...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx690
更新日期:2017-09-29 00:00:00
abstract::Plants have large diverse families of small secreted proteins (SSPs) that play critical roles in the processes of development, differentiation, defense, flowering, stress response, symbiosis, etc. Oryza sativa is one of the major crops worldwide and an excellent model for monocotyledonous plants. However, there had no...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1090
更新日期:2013-01-01 00:00:00
abstract::PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron-exon organization and provides valuable insights into the evolution of gene structure in plant genomes. Recent...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw935
更新日期:2017-01-04 00:00:00
abstract::Transcription of the bacteriophage Mu mom operon requires transactivation by the phage-encoded C protein. DNase I footprinting showed that in the absence of C, Escherichia coli RNA polymerase E(sigma)70 (RNAP) binds to the mom promoter (Pmom) region at a site, P2 (from -64 to -11 with respect to the transcription star...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/24.20.4042
更新日期:1996-10-15 00:00:00
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::We have developed a simple but powerful method and web server to quickly locate charged and hydrophobic clusters in proteins (http://www.netasa.org/qgrid/index.html). For the charged clusters, each atom in the protein is first assigned a charge according to a standard force field. Then a box is created with dimensions...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh363
更新日期:2004-07-01 00:00:00
abstract::The location of proteins on the mitochondrial DNA (mtDNA) of Drosophila virilis was investigated by Me3 psoralen photoreaction of mitochondria isolated from embryos. After photoreaction the mtDNA was purified and the pattern of DNA cross-linking was determined by electron microscopy of the DNA under totally denaturing...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.4.1991
更新日期:1984-02-24 00:00:00
abstract::Melibiose uptake and hydrolysis in E.coli is performed by the MelB and MelA proteins, respectively. We report the cloning and sequencing of the melA gene. The nucleotide sequence data showed that melA codes for a 450 amino acid long protein with a molecular weight of 50.6 kd. The sequence data also supported the assum...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/15.5.2213
更新日期:1987-03-11 00:00:00