Abstract:
:MiRNAs are important regulators of gene expression and are frequently deregulated under pathologic conditions. They are highly stable in bodily fluids which makes them feasible candidates to become minimally invasive biomarkers. In fact, several studies already proposed circulating miRNA-based biomarkers for different types of neoplastic, cardiovascular and degenerative diseases. However, many of these studies rely on small RNA sequencing experiments that are based on different RNA extraction and processing protocols, rendering results incomparable. We generated liqDB, a database for liquid biopsy small RNA sequencing profiles that provides users with meaningful information to guide their small RNA liquid biopsy research and to overcome technical and conceptual problems. By means of a user-friendly web interface, miRNA expression profiles from 1607 manually annotated samples can be queried and explored at different levels. Result pages include downloadable expression matrices, differential expression analysis, most stably expressed miRNAs, cluster analysis and relevant visualizations by means of boxplots and heatmaps. We anticipate that liqDB will be a useful tool in liquid biopsy research as it provides a consistently annotated large compilation of experiments together with tools for reproducible analysis, comparison and hypothesis generation. LiqDB is available at http://bioinfo5.ugr.es/liqdb.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Aparicio-Puerta E,Jáspez D,Lebrón R,Koppers-Lalic D,Marchal JA,Hackenberg Mdoi
10.1093/nar/gky981subject
Has Abstractpub_date
2019-01-08 00:00:00pages
D113-D120issue
D1eissn
0305-1048issn
1362-4962pii
5144140journal_volume
47pub_type
杂志文章abstract::The circadian clock comprises transcriptional feedback loops of clock genes. Cryptochromes are essential components of the negative feedback loop in mammals as they inhibit CLOCK-BMAL1-mediated transcription. We purified mouse CRY1 (mCRY1) protein complexes from Sarcoma 180 cells to determine their roles in circadian ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn1013
更新日期:2009-03-01 00:00:00
abstract::Polynucleotides containing adenosine and 8-azidoadenosine or inosine and 8-azidoinosine residues have been prepared from mixtures of nucleoside diphosphates using polynucleotide phosphorylase from Escherichia coli. These copolymers can form complexes with polyuridylic or polycytidylic acids respectively. Single strand...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/8.7.1675
更新日期:1980-04-11 00:00:00
abstract::Treatment of responsive cells by interferons (IFNs) induces within a few hours a rise in the concentration of several proteins and mRNAs. In order to characterize these IFN-induced mRNA species, we have cloned in E. coli the cDNA made from a 17-18S poly(A)+ RNA of human fibroblastoid cells (SV80) treated with IFN-beta...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/11.5.1213
更新日期:1983-03-11 00:00:00
abstract::The early DNa products of reverse transcription have been analyzed from reconstructed reactions containing avian myeloblastosis virus 35S RNA . tRNAtrp complex and highly purified reverse transcriptase. We describe conditions for the synthesis of genome-length complementary DNA and two discrete species of plus strand ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.3.1009
更新日期:1982-02-11 00:00:00
abstract::Uracil-Specific Exision Reagent (USER) fusion is a recently developed technique that allows for assembly of multiple DNA fragments in a few simple steps. However, designing primers for USER fusion is both tedious and time consuming. Here, we present the Primer Help for USER (PHUSER) software, a novel tool for designin...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr394
更新日期:2011-07-01 00:00:00
abstract::Alternative splicing and polyadenylation were observed pervasively in eukaryotic messenger RNAs. These alternative isoforms could either be consequences of physiological regulation or stochastic noise of RNA processing. To quantify the extent of stochastic noise in splicing and polyadenylation, we analyzed the alterna...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks1271
更新日期:2013-02-01 00:00:00
abstract::The International Committee on Taxonomy of Viruses (ICTV) is charged with the task of developing, refining, and maintaining a universal virus taxonomy. This task encompasses the classification of virus species and higher-level taxa according to the genetic and biological properties of their members; naming virus taxa;...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx932
更新日期:2018-01-04 00:00:00
abstract::The human beta-actin promoter, including its 5' flanking region and 5' untranslated region, is ubiquitously active in mammalian cells in culture. In this report we investigated the transcriptional activity of, and the protein-DNA interactions that occur within, the proximal region of the human beta-actin promoter. Eff...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.24.6913
更新日期:1991-12-25 00:00:00
abstract::The products of many bacterial non-ribosomal peptide synthetases (NRPS) are highly important secondary metabolites, including vancomycin and other antibiotics. The ability to predict substrate specificity of newly detected NRPS Adenylation (A-) domains by genome sequencing efforts is of great importance to identify an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr323
更新日期:2011-07-01 00:00:00
abstract::Here we employ a set of RNA Polymerase II (Pol II) activity mutants to determine the consequences of increased or decreased Pol II catalysis on gene expression in Saccharomyces cerevisiae. We find that alteration of Pol II catalytic rate, either fast or slow, leads to decreased Pol II occupancy and apparent reduction ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx037
更新日期:2017-05-05 00:00:00
abstract::We present the results of in vitro binding studies aimed at defining the key recognition elements on the MS2 RNA translational operator (TR) essential for complex formation with coat protein. We have used chemically synthesized operators carrying modified functional groups at defined nucleotide positions, which are es...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.13.2512
更新日期:1995-07-11 00:00:00
abstract::Isopentenyl adenosine derivatives are always located adjacent to the 3' end of the anticodon in transfer RNA and have been implicated in certain biological functions. In the enteric bacterium, E. coli, the derivative is ms2i6A whereas in some plant associated bacteria the derivative is the hydroxylated form, ms2io6A. ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.18.5663
更新日期:1982-09-25 00:00:00
abstract::We investigated how Escherichia coli ClpXP targets the helicase-nuclease (HsdR) subunit of the bacterial Type I restriction-modification enzyme EcoKI during restriction alleviation (RA). RA is a temporary reduction in endonuclease activity that occurs when Type I enzymes bind unmodified recognition sites on the host g...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gku851
更新日期:2014-10-29 00:00:00
abstract::The database of imprinted genes and parent-of-origin effects in animals (http://www.otago.ac.nz/IGC ) is a collation of genes and phenotypes for which parent-of-origin effects have been reported. The database currently includes over 220 entries, which describe over 40 imprinted genes in human, mouse and other animals....
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.1.275
更新日期:2001-01-01 00:00:00
abstract::The Protein Data Bank in Europe (PDBe, pdbe.org) is actively engaged in the deposition, annotation, remediation, enrichment and dissemination of macromolecular structure data. This paper describes new developments and improvements at PDBe addressing three challenging areas: data enrichment, data dissemination and func...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1070
更新日期:2018-01-04 00:00:00
abstract::The gene co-expression analysis toolbox (GeneCAT) introduces several novel microarray data analyzing tools. First, the multigene co-expression analysis, combined with co-expressed gene networks, provides a more powerful data mining technique than standard, single-gene co-expression analysis. Second, the high-throughpu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkn292
更新日期:2008-07-01 00:00:00
abstract::We have studied the coil-to-helix transition of the DNA oligomer d(C4A4T4C4), using circular dichroism measurements to monitor the formation of A.T base pairs within the central self-complementary A4T4 region and the formation of protonated C.C+ base pairs at the ends of the oligomer. We found that both A.T and C.C+ b...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/12.19.7565
更新日期:1984-10-11 00:00:00
abstract::MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of methylation data. Here, we present an updated implementation of MethBank (version 3.0) by incorporating more DNA methylomes from multi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1139
更新日期:2018-01-04 00:00:00
abstract::U4 RNA from chicken, rat and man was examined for nucleotide sequence and secondary structure. Three molecular species, U4A, U4B and U4C were detected in the three animal species. U4A is 146 nucleotide long and U4B RNA only lacks the 3' terminal G. four nucleotides are missing at the 3'-end of U4C RNA which, in additi...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/9.12.2699
更新日期:1981-06-25 00:00:00
abstract::Alternative splicing (AS) and alternative polyadenylation (APA) generate diverse transcripts in mammalian genomes during development and differentiation. Epigenetic marks such as trimethylation of histone H3 lysine 36 (H3K36me3) and DNA methylation play a role in generating transcriptome diversity. Intragenic CpG isla...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa556
更新日期:2020-09-04 00:00:00
abstract::Replication Factor C (RF-C) of Saccharomyces cerevisiae is a complex that consists of several different polypeptides ranging from 120- to 37 kDa (Yoder and Burgers, 1991; Fien and Stillman, 1992), similar to human RF-C. We have isolated a gene, RFC2, that appears to be a component of the yeast RF-C. The RFC2 gene is l...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/22.9.1527
更新日期:1994-05-11 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::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::DNA dodecamers have been designed with two cytosines on each end and intervening A and T stretches, such that the oligomers have fully complementary A:T base pairs when aligned in the parallel orientation. Spectroscopic (UV, CD and IR), NMR and molecular dynamics studies have shown that oligomers having the sequences ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/30.7.1500
更新日期:2002-04-01 00:00:00
abstract::The FREP database (http://facts.gsc.riken.go.jp/FREP/) contains 31 396 RepeatMasker-identified non-redundant variant repeat sequences derived from 16,527 mouse cDNAs with protein-coding potential. The repeats were computationally associated with potential effects on transcriptional variation, translation, protein func...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkh123
更新日期:2004-01-01 00:00:00
abstract::TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkl1043
更新日期:2007-01-01 00:00:00
abstract::A cell-free extract of yeast nuclei that can specifically transcribe cloned yeast 5S rRNA genes has been developed. Optima for transcription of 5S rDNA were determined and conditions of extract preparation leading to reproducible activities and specificities established. The major in vitro product has the same size an...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/10.17.5223
更新日期:1982-09-11 00:00:00
abstract::This paper examines theoretically the effects that restraints on the tertiary structure of a superhelical DNA domain exert on the energetics of linking and the onset of conformational transitions. The most important tertiary constraint arises from the nucleosomal winding of genomic DNA in vivo. Conformational transiti...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/15.23.9985
更新日期:1987-12-10 00:00:00
abstract::Melanotransferrin (MTf) is a tumor associated antigen found in abundance on the surface of melanoma cells. It is a transferrin-like protein found in low amount in most adult tissues and whose gene is reminiscent of house-keeping genes. With the goal of understanding the regulatory mechanisms which might explain the en...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.11.2853
更新日期:1992-06-11 00:00:00
abstract::The determination of distances between specific points in nucleic acids is essential to understanding their behaviour at the molecular level. The ability to measure distances of 2-10 nm is particularly important: deformations arising from protein binding commonly fall within this range, but the reliable measurement of...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa086
更新日期:2020-04-06 00:00:00