Abstract:
:The Gene Expression Atlas (http://www.ebi.ac.uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease states, sample treatments and other biological/experimental conditions. The content of this database derives from curation, re-annotation and statistical analysis of selected data from the ArrayExpress Archive of Functional Genomics Data. A simple interface allows the user to query for differential gene expression either (i) by gene names or attributes such as Gene Ontology terms, or (ii) by biological conditions, e.g. diseases, organism parts or cell types. The gene queries return the conditions where expression has been reported, while condition queries return which genes are reported to be expressed in these conditions. A combination of both query types is possible. The query results are ranked using various statistical measures and by how many independent studies in the database show the particular gene-condition association. Currently, the database contains information about more than 200,000 genes from nine species and almost 4500 biological conditions studied in over 30,000 assays from over 1000 independent studies.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Kapushesky M,Emam I,Holloway E,Kurnosov P,Zorin A,Malone J,Rustici G,Williams E,Parkinson H,Brazma Adoi
10.1093/nar/gkp936subject
Has Abstractpub_date
2010-01-01 00:00:00pages
D690-8issue
Database issueeissn
0305-1048issn
1362-4962pii
gkp936journal_volume
38pub_type
杂志文章abstract::The thermal denaturation spectra of E. coli 50s and 30s ribosomal sub units and of their isolated RNA's were studied over the wavelength range of 2300-3000 Angstrom. It was possible to fit the experimental denaturation spectra with super positions of the reference spectra for denaturation of A - U and G - C base pairs...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/2.3.373
更新日期:1975-03-01 00:00:00
abstract::COMPASS is a method for homology detection and local alignment construction based on the comparison of multiple sequence alignments (MSAs). The method derives numerical profiles from given MSAs, constructs local profile-profile alignments and analytically estimates E-values for the detected similarities. Until now, CO...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm293
更新日期:2007-07-01 00:00:00
abstract::Post-transcriptional methylation of ribose at position O-2' is one of the most common and conserved types of RNA modification. Details of the functional roles of these methylations are far from clear, although in tRNA they are involved at position 34 in regulation of codon recognition and in eukaryotic rRNAs they are ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.18.e20
更新日期:1999-09-15 00:00:00
abstract::Sensitive detection of microsatellite instability (MSI) in tissue or liquid biopsies using next generation sequencing (NGS) has growing prognostic and predictive applications in cancer. However, the complexities of NGS make it cumbersome as compared to established multiplex-PCR detection of MSI. We present a new appro...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa1175
更新日期:2020-12-08 00:00:00
abstract::DNA methylation of cytosine in eukaryotic cells is a common epigenetic modification, which plays an important role in gene expression and thus affects various cellular processes like development and carcinogenesis. The occurrence of 5-methyl-2'-deoxycytosine (5mC) as well as the distribution pattern of this epigenetic...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkw812
更新日期:2016-11-16 00:00:00
abstract::Alternative splicing of mRNA precursors results in multiple protein variants from a single gene and is critical for diverse cellular processes and development. Xist encodes a long noncoding RNA which is a central player to induce X-chromosome inactivation in female mammals and has two major splicing variants: long and...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1227
更新日期:2018-03-16 00:00:00
abstract::High density oligonucleotide array technology is widely used in many areas of biomedical research for quantitative and highly parallel measurements of gene expression. Affymetrix GeneChip arrays are the most popular. In this technology each gene is typically represented by a set of 11-20 pairs of probes. In order to o...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gng015
更新日期:2003-02-15 00:00:00
abstract::We have analyzed the ATPase activity exhibited by the UvrABC DNA repair complex. The UvrA protein is an ATPase whose lack of DNA dependence may be related to the ATP induced monomer-dimer transitions. ATP induced dimerization may be responsible for the enhanced DNA binding activity observed in the presence of ATP. Alt...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/17.11.4145
更新日期:1989-06-12 00:00:00
abstract::The iProClass database provides comprehensive, value-added descriptions of proteins and serves as a framework for data integration in a distributed networking environment. The protein information in iProClass includes family relationships as well as structural and functional classifications and features. The current v...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg044
更新日期:2003-01-01 00:00:00
abstract::The spatio-temporal organization of chromatin in the eukaryotic cell nucleus is of vital importance for transcription, DNA replication and genome maintenance. Each of these activities is tightly regulated in both time and space. While we have a good understanding of chromatin organization in space, for example in fixe...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkaa135
更新日期:2020-04-17 00:00:00
abstract::Yeast two-hybrid (Y2H) screenings result in identification of many out-of-frame (OOF) clones that code for short (2-100 amino acids) peptides with no sequence homology to known proteins. We hypothesize that these peptides can reveal common short linear motifs (SLiMs) responsible for their selection. We present a new p...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr600
更新日期:2011-10-01 00:00:00
abstract::Fluoropyrimidines, such as 5-fluorouracil (5-FU), are used extensively in cancer therapy. In the cell, 5-FU is metabolized to 5-fluorodeoxyuridylate (5-FdUMP), a tight binding covalent inhibitor of thymidylate synthase (TS). In order to create 5-FdUMP resistant enzymes to protect chemosensitive normal cells and furthe...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.18.3702
更新日期:1999-09-15 00:00:00
abstract::The ability of histone chaperone Anti-silencing factor 1 (Asf1) to direct acetylation of lysine 56 of histone H3 (H3K56ac) represents an important regulatory step in genome replication and DNA repair. In Saccharomyces cerevisiae, Asf1 interacts functionally with a second chaperone, Vps75, and the lysine acetyltransfer...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz508
更新日期:2019-08-22 00:00:00
abstract::Initiation of Adenovirus (Ad) DNA replication occurs by a protein-priming mechanism in which the viral precursor terminal protein (pTP) and DNA polymerase (pol) as well as two nuclear DNA-binding proteins from uninfected HeLa cells are required. Biochemical studies on the pTP and DNA polymerase proteins separately hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/16.6.2431
更新日期:1988-03-25 00:00:00
abstract::We previously found that the splicing of exon 5 to exon 6 in the rat beta-TM gene required that exon 6 first be joined to the downstream common exon 8 (Helfman et al., Genes and Dev. 2, 1627-1638, 1988). Pre-mRNAs containing exon 5, intron 5 and exon 6 are not normally spliced in vitro. We have carried out a mutationa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.12.2318
更新日期:1994-06-25 00:00:00
abstract::A simple method, primer specific and mispair extension analysis (PSMEA) with pfu DNA polymerase was developed for genotyping. PSMEA is based on the unique properties of 3'-->5' exonuclease proofreading activity. In the presence of an incomplete set of dNTPs, pfu was found to be extremely discriminative in nucleotide i...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.21.5013
更新日期:1998-11-01 00:00:00
abstract::Large-scale sequencing studies discovered substantial genetic variants occurring in enhancers which regulate genes via long range chromatin interactions. Importantly, such variants could affect enhancer regulation by changing transcription factor bindings or enhancer hijacking, and in turn, make an essential contribut...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx920
更新日期:2018-01-04 00:00:00
abstract::Sequence-specific interactions between aminoacyl-tRNA synthetases and their cognate tRNAs ensure both accurate RNA recognition and the efficient catalysis of aminoacylation. The effects of tRNA(Trp)variants on the aminoacylation reaction catalyzed by wild-type Escherichia coli tryptophanyl-tRNA synthe-tase (TrpRS) hav...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/27.18.3631
更新日期:1999-09-15 00:00:00
abstract::With an increased emphasis on genotyping of single nucleotide polymorphisms (SNPs) in disease association studies, the genotyping platform of choice is constantly evolving. In addition, the development of more specific SNP assays and appropriate genotype validation applications is becoming increasingly critical to elu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gnh046
更新日期:2004-03-26 00:00:00
abstract::U1 snRNP plays a crucial role in the 5' splice site recognition during splicing. Here we report the first example of naturally occurring U1-independent U2-type splicing in humans. The U1 components were not included in the pre-spliceosomal E complex formed on the human F1gamma (hF1gamma) intron 9 in vitro. Moreover, h...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp050
更新日期:2009-04-01 00:00:00
abstract::Nuclei isolated from cultured mouse and rat cell lines initiated pre-rRNA chains at the correct site and with the correct nucleotide specificity (A for mouse, G for rat). Nucleic acid filter hybridization and S1 nuclease mapping were used to analyze the RNA products initiated with nucleoside (beta-S)triphosphates. Ini...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.21.8115
更新日期:1984-11-12 00:00:00
abstract::Mycobacterium tuberculosis (Mtb) Cmr (Rv1675c) is a CRP/FNR family transcription factor known to be responsive to cAMP levels and during macrophage infections. However, Cmr's DNA binding properties, cellular targets and overall role in tuberculosis (TB) complex bacteria have not been characterized. In this study, we u...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv889
更新日期:2016-01-08 00:00:00
abstract::The synthesis of stable RNA in Mycoplasma capricolum was studied by [32P] labeling of cellular RNA of cells grown in a partially-defined medium in the presence or absence of an amino acid mixture supplement. The results indicate that M. capricolum employs the same stringent control mechanism used by E. coli cells, as ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.15.3641
更新日期:1981-08-11 00:00:00
abstract::Modular primers are strings of three contiguously annealed unligated oligonucleotides (modules) as short as 5- or 6-mers, selected from a presynthesized library. It was previously found that such strings can prime DNA sequencing reactions specifically, thus eliminating the need for the primer synthesis step in DNA seq...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.15.2881
更新日期:1995-08-11 00:00:00
abstract::In Xenopus oocytes in vitro transcribed mouse U7 RNA is assembled into small nuclear ribonucleoproteins (snRNPs) that are functional in histone RNA 3' processing. If the special Sm binding site of U7 (AAUUUGUCUAG, U7 Sm WT) is converted into the canonical Sm sequence derived from the major snRNAs (AAUUUUUGGAG, U7 Sm O...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.16.3141
更新日期:1995-08-25 00:00:00
abstract::The generalized mismatch repair system of Streptococcus pneumoniae (the Hex system) can eliminate base pair mismatches arising in heteroduplex DNA during transformation or by DNA polymerase errors during replication. Mismatch repair is most likely initiated at nicks or gaps. The present work was started to examine the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.20.5525
更新日期:1991-10-25 00:00:00
abstract::Modified bases, such as O6-methylguanines, are produced in cells exposed to alkylating agents and cause apoptosis. In human cells treated with N-methyl-N-nitrosourea, we detected a protein complex composed of MutSalpha, MutLalpha and PCNA on damaged DNA by immunoprecipitation method using chromatin extracts, in which ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki878
更新日期:2005-10-04 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::The regulation of the Sso II restriction-modification system from Shigella sonnei was studied in vivo and in vitro . In lacZ fusion experiments, Sso II methyltransferase (M. Sso II) was found to repress its own synthesis but stimulate expression of the cognate restriction endonuclease (ENase). The N-terminal 72 amino ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.11.2114
更新日期:1997-06-01 00:00:00
abstract::The finding in animal species of complexes homologous to the products of six Saccharomyces cerevisiae genes, origin of replication recognition complex (ORC), has suggested that ORC-related mechanisms have been conserved in all eukaryotes. In plants, however, the only cloned putative homologs of ORC subunits are the Ar...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkg138
更新日期:2003-01-15 00:00:00