Abstract：
:Bgee is a database to retrieve and compare gene expression patterns in multiple animal species, produced by integrating multiple data types (RNA-Seq, Affymetrix, in situ hybridization, and EST data). It is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of normal gene expression. Curation includes very large datasets such as GTEx (re-annotation of samples as 'healthy' or not) as well as many small ones. Data are integrated and made comparable between species thanks to consistent data annotation and processing, and to calls of presence/absence of expression, along with expression scores. As a result, Bgee is capable of detecting the conditions of expression of any single gene, accommodating any data type and species. Bgee provides several tools for analyses, allowing, e.g., automated comparisons of gene expression patterns within and between species, retrieval of the prefered conditions of expression of any gene, or enrichment analyses of conditions with expression of sets of genes. Bgee release 14.1 includes 29 animal species, and is available at https://bgee.org/ and through its Bioconductor R package BgeeDB.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Bastian FB,Roux J,Niknejad A,Comte A,Fonseca Costa SS,de Farias TM,Moretti S,Parmentier G,de Laval VR,Rosikiewicz M,Wollbrett J,Echchiki A,Escoriza A,Gharib WH,Gonzales-Porta M,Jarosz Y,Laurenczy B,Moret P,Person E,doi
10.1093/nar/gkaa793subject
Has Abstractpub_date
2021-01-08 00:00:00pages
D831-D847issue
D1eissn
0305-1048issn
1362-4962pii
5920517journal_volume
49pub_type
杂志文章abstract：:The yeast protein Rrf1p encoded by the FIL1 nuclear gene bears significant sequence similarity to Escherichia coli ribosome recycling factor (RRF). Here, we call FIL1 Ribosome Recycling Factor of yeast, RRF1. Its gene product, Rrf1p, was localized in mitochondria. Deletion of RRF1 leads to a respiratory incompetent ph...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkg449
更新日期：2003-07-15 00:00:00
abstract：:Human stem cells are promising sources for regenerative therapy. To ensure safety of future therapeutic applications, the differentiation potency of stem cells has to be tested and be widely opened to the public. The potency is generally assessed by teratoma formation comprising differentiated cells from all three ger...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1096
更新日期：2016-01-04 00:00:00
abstract：:A dot hybridization method is presented for rapidly determining the relative concentrations of nucleic acids in a mixture, as well as the extent of sequence homology between related RNA or DNA species. ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/7.6.1541
更新日期：1979-11-24 00:00:00
abstract：:Bacillus subtilis OhrR is a dimeric repressor that senses organic peroxides and regulates the expression of the OhrA peroxiredoxin. Derepression results from oxidation of an active site cysteine which ultimately results in formation of a mixed disulfide with a low molecular weight thiol, a cyclic sulfenamide, or overo...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkn1052
更新日期：2009-03-01 00:00:00
abstract：:DNA supercoiling is an important regulator of gene activity. The transmission of transcription-generated supercoiling wave along a DNA helix provides a way for a gene being transcribed to communicate with and regulate its neighboring genes. Currently, the dynamic behavior of supercoiling transmission remains unclear o...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky534
更新日期：2018-08-21 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：:Using a partially purified replication complex from tobacco chloroplasts, replication origins have been localized to minimal sequences of 82 (pKN8, positions 137 683-137 764) and 243 bp (pKN3, positions 130 513-130 755) for ori A and ori B respectively. Analysis of in vitro replication products by two-dimensional agar...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/25.18.3681
更新日期：1997-09-15 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：:The promoter of the human BCR gene, regulating the transcription of the chimeric BCR/ABL mRNA in leukemia, has been isolated and characterized. A region of 1.1 kb immediately 5' to the transcription start site was analyzed in detail by sequencing, DNase 1 footprinting, gel retardation and functional studies. These exp...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/18.23.7119
更新日期：1990-12-11 00:00:00
abstract：:Peptides of defined length carrying a diazirine photoaffinity label attached either to the alpha-NH2 group of the N-terminal methionine residue, or to the epsilon-NH2 group of an immediately adjacent lysine residue, were prepared in situ on Escherichia coli ribosomes in the presence of a synthetic mRNA analogue. Pepti...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/22.8.1394
更新日期：1994-04-25 00:00:00
abstract：:Post-transcriptional modifications in archaeal RNA are known to be phylogenetically distinct but relatively little is known of tRNA from the Methanococci, a lineage of methanogenic marine euryarchaea that grow over an unusually broad temperature range. Transfer RNAs from Methanococcus vannielii, Methanococcus maripalu...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/29.22.4699
更新日期：2001-11-15 00:00:00
abstract：:Adenosine deaminases that act on RNA (ADARs) convert adenosine to inosine within double-stranded regions of RNA, resulting in increased transcriptomic diversity, as well as protection of cellular double-stranded RNA (dsRNA) from silencing and improper immune activation. The presence of dsRNA-binding domains (dsRBDs) i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky800
更新日期：2018-10-12 00:00:00
abstract：:The HSV gene encoding ICP4 is negatively regulated and the HSV gene encoding thymidine kinase is positively regulated by ICP4 in vivo. We report that ICP4 is a component of a stable complex that contains protein and a sequence of approximately 28 nucleotides that span the ICP4 gene transcription initiation site. The a...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.2.555
更新日期：1988-01-25 00:00:00
abstract：:During protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5A (a/eIF-5A) and in bacteria by the homologous protein EF-P. While a structure of EF-P bound to the 70S ribosome exists, structural insight into eIF-5A on ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1517
更新日期：2016-02-29 00:00:00
abstract：:A new method is described for the direct construction of randomly mutagenized genes by applying the polymerase chain reaction (PCR) to an oligonucleotide synthesized using doped nucleotide reservoirs. We have demonstrated the utility of this method by generating a library of mutant HIV-1 tat genes. Several arbitrarily...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/20.20.5311
更新日期：1992-10-25 00:00:00
abstract：:Human Protein Reference Database (HPRD) (http://www.hprd.org) was developed to serve as a comprehensive collection of protein features, post-translational modifications (PTMs) and protein-protein interactions. Since the original report, this database has increased to >20 000 proteins entries and has become the largest...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkj141
更新日期：2006-01-01 00:00:00
abstract：:Explicit solvent molecular dynamics (MD) was used to describe the intrinsic flexibility of the helix 42-44 portion of the 23S rRNA (abbreviated as Kt-42+rGAC; kink-turn 42 and GTPase-associated center rRNA). The bottom part of this molecule consists of alternating rigid and flexible segments. The first flexible segmen...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkm245
更新日期：2007-01-01 00:00:00
abstract：:A flow-injection (FI) device is combined, through the use of a low-volume (4 microl) flow cell, with an ultrasensitive surface plasmon resonance (SPR) spectrometer equipped with a bi-cell photodiode detector. The application of this novel FI-SPR device for sequence-specific ultratrace analysis of oligodeoxynucleotides...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gnf072
更新日期：2002-07-15 00:00:00
abstract：:Heterotrimeric eukaryotic/archaeal translation initiation factor 2 (e/aIF2) binds initiator methionyl-tRNA and plays a key role in the selection of the start codon on messenger RNA. tRNA binding was extensively studied in the archaeal system. The γ subunit is able to bind tRNA, but the α subunit is required to reach h...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gks1180
更新日期：2013-01-01 00:00:00
abstract：:We describe improve enzymatic methods for sequencing method for sequencing DNA. They are based on partial digestion of duplex DNA with exonuclease III to produce DNA molecules with 3' ends shortened to varying lengths, followed by repair synthesis to extend and label the 3' ends. After asymmetrical cleavage of the DNA...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/10.6.2065
更新日期：1982-03-25 00:00:00
abstract：:Numerous eukaryotic genes are alternatively spliced. Recently, deep transcriptome sequencing has skyrocketed proportion of alternatively spliced genes; over 95% human multi-exon genes are alternatively spliced. One fundamental question is: are all these alternative splicing (AS) events functional? To look into this is...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gku1253
更新日期：2014-12-16 00:00:00
abstract：:Stability of aromatic phosphoramidates was studied using 2',3'-O-dibenzoyluridine 5'-phosphoramidates and N,2',3'-O-tribenzoylcytidine 5'-phosphate. The effect of dicyclohexylcarbodiimide in this mixture was investigated. Decomposition of the anilidate was slower in the presence of DCC. Substituted anilidates of uridi...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/1.2.223
更新日期：1974-02-01 00:00:00
abstract：:From gene expression to nanotechnology, understanding and controlling DNA requires a detailed knowledge of its higher order structure and dynamics. Here we take advantage of the environment-sensitive photoisomerization of cyanine dyes to probe local and global changes in DNA structure. We report that a covalently atta...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gky887
更新日期：2018-11-30 00:00:00
abstract：:NikR is a transcriptional metalloregulator central in the mandatory response to acidity of Helicobacter pylori that controls the expression of numerous genes by binding to specific promoter regions. NikR/DNA interactions were proposed to rely on protein activation by Ni(II) binding to high-affinity (HA) and possibly s...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp1216
更新日期：2010-05-01 00:00:00
abstract：:Transcription factors (TFs) are sequence-specific DNA-binding proteins acting as critical regulators of gene expression. The Plant Promoter Analysis Navigator (PlantPAN; http://PlantPAN2.itps.ncku.edu.tw) provides an informative resource for detecting transcription factor binding sites (TFBSs), corresponding TFs, and ...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkv1035
更新日期：2016-01-04 00:00:00
abstract：:Immunoglobulin genes contain a conserved eight base sequence element 5' to the site of transcription initiation. This octamer can serve as a site for the binding of nuclear proteins which are presumably involved in the cell type specific expression of this family of genes. In studying the binding of nuclear proteins t...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/16.12.5503
更新日期：1988-06-24 00:00:00
abstract：:Protein structures often show similarities to another which would not be seen at the sequence level. Given the coordinates of a protein chain, the SALAMI server at www.zbh.uni-hamburg.de/salami will search the protein data bank and return a set of similar structures without using sequence information. The results page...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkp431
更新日期：2009-07-01 00:00:00
abstract：:We have developed an effective post-PCR sterilization process and have applied the procedure to a diagnostic assay for HIV-1. The method, which is based on isopsoralen photochemistry, satisfies both the inactivation and hybridization requirements of a practical sterilization process. The key feature of the technique i...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/19.1.109
更新日期：1991-01-11 00:00:00
abstract：:Twenty AdoMet-dependent methyltransferases (MTases) have been characterized structurally by X-ray crystallography and NMR. These include seven DNA MTases, five RNA MTases, four protein MTases and four small molecule MTases acting on the carbon, oxygen or nitrogen atoms of their substrates. The MTases share a common co...
journal_title：Nucleic acids research
pub_type： 杂志文章,评审
doi：10.1093/nar/29.18.3784
更新日期：2001-09-15 00:00:00
abstract：:SIRT6 is critical for activating transcription of Nuclear factor (erythroid-derived 2)-like 2 (NRF2) responsive genes during oxidative stress. However, while the mechanism of SIRT6-mediated silencing is well understood, the mechanism of SIRT6-mediated transcriptional activation is unknown. Here, we employed SIRT6 sepa...
journal_title：Nucleic acids research
pub_type： 杂志文章
doi：10.1093/nar/gkz528
更新日期：2019-09-05 00:00:00
