YM500: a small RNA sequencing (smRNA-seq) database for microRNA research.


:MicroRNAs (miRNAs) are small RNAs ∼22 nt in length that are involved in the regulation of a variety of physiological and pathological processes. Advances in high-throughput small RNA sequencing (smRNA-seq), one of the next-generation sequencing applications, have reshaped the miRNA research landscape. In this study, we established an integrative database, the YM500 (http://ngs.ym.edu.tw/ym500/), containing analysis pipelines and analysis results for 609 human and mice smRNA-seq results, including public data from the Gene Expression Omnibus (GEO) and some private sources. YM500 collects analysis results for miRNA quantification, for isomiR identification (incl. RNA editing), for arm switching discovery, and, more importantly, for novel miRNA predictions. Wetlab validation on >100 miRNAs confirmed high correlation between miRNA profiling and RT-qPCR results (R = 0.84). This database allows researchers to search these four different types of analysis results via our interactive web interface. YM500 allows researchers to define the criteria of isomiRs, and also integrates the information of dbSNP to help researchers distinguish isomiRs from SNPs. A user-friendly interface is provided to integrate miRNA-related information and existing evidence from hundreds of sequencing datasets. The identified novel miRNAs and isomiRs hold the potential for both basic research and biotech applications.


Nucleic Acids Res


Nucleic acids research


Cheng WC,Chung IF,Huang TS,Chang ST,Sun HJ,Tsai CF,Liang ML,Wong TT,Wang HW




Has Abstract


2013-01-01 00:00:00




Database issue










  • iGNM 2.0: the Gaussian network model database for biomolecular structural dynamics.

    abstract::Gaussian network model (GNM) is a simple yet powerful model for investigating the dynamics of proteins and their complexes. GNM analysis became a broadly used method for assessing the conformational dynamics of biomolecular structures with the development of a user-friendly interface and database, iGNM, in 2005. We pr...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Li H,Chang YY,Yang LW,Bahar I

    更新日期:2016-01-04 00:00:00

  • A positioned +1 nucleosome enhances promoter-proximal pausing.

    abstract::Chromatin distribution is not uniform along the human genome. In most genes there is a promoter-associated nucleosome free region (NFR) followed by an array of nucleosomes towards the gene body in which the first (+1) nucleosome is strongly positioned. The function of this characteristic chromatin distribution in tran...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Jimeno-González S,Ceballos-Chávez M,Reyes JC

    更新日期:2015-03-31 00:00:00

  • Nucleotide excision repair efficiency in quiescent human fibroblasts is modulated by circadian clock.

    abstract::The efficiency of Nucleotide Excision Repair (NER)process is crucial for maintaining genomic integrity because in many organisms, including humans, it represents the only system able to repair a wide range of DNA damage. The aim of the work was to investigate whether the efficiency of the repair of photoproducts induc...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Bee L,Marini S,Pontarin G,Ferraro P,Costa R,Albrecht U,Celotti L

    更新日期:2015-02-27 00:00:00

  • The ATP-mediated formation of the YgjD-YeaZ-YjeE complex is required for the biosynthesis of tRNA t6A in Escherichia coli.

    abstract::The essential and universal N(6)-threonylcarbamoyladenosine (t(6)A) modification at position 37 of ANN-decoding tRNAs plays a pivotal role in translational fidelity through enhancement of the cognate codon recognition and stabilization of the codon-anticodon interaction. In Escherichia coli, the YgjD (TsaD), YeaZ (Tsa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhang W,Collinet B,Perrochia L,Durand D,van Tilbeurgh H

    更新日期:2015-02-18 00:00:00

  • Dicer cleaves 5'-extended microRNA precursors originating from RNA polymerase II transcription start sites.

    abstract::MicroRNAs (miRNAs) are approximately 22 nucleotide (nt) long and play important roles in post-transcriptional regulation in both plants and animals. In animals, precursor (pre-) miRNAs are ∼70 nt hairpins produced by Drosha cleavage of long primary (pri-) miRNAs in the nucleus. Exportin-5 (XPO5) transports pre-miRNAs ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sheng P,Fields C,Aadland K,Wei T,Kolaczkowski O,Gu T,Kolaczkowski B,Xie M

    更新日期:2018-06-20 00:00:00

  • Promoter and enhancer activities of long terminal repeats associated with cellular retrovirus-like (VL30) elements.

    abstract::LTR units associated with cellular retrovirus-like elements are abundantly present in chromosomal DNA of animal cells. We have analyzed the promoter and enhancer activities of diverse LTR units associated with different members of the murine retrovirus-like family known as VL30. We report here that the structurally he...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rotman G,Itin A,Keshet E

    更新日期:1986-01-24 00:00:00

  • NOPdb: Nucleolar Proteome Database.

    abstract::The Nucleolar Proteome Database (NOPdb) archives data on >700 proteins that were identified by multiple mass spectrometry (MS) analyses from highly purified preparations of human nucleoli, the most prominent nuclear organelle. Each protein entry is annotated with information about its corresponding gene, its domain st...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Leung AK,Trinkle-Mulcahy L,Lam YW,Andersen JS,Mann M,Lamond AI

    更新日期:2006-01-01 00:00:00

  • Differential effects of hnRNP D/AUF1 isoforms on HIV-1 gene expression.

    abstract::Control of RNA processing plays a major role in HIV-1 gene expression. To explore the role of several hnRNP proteins in this process, we carried out a siRNA screen to examine the effect of depletion of hnRNPs A1, A2, D, H, I and K on HIV-1 gene expression. While loss of hnRNPs H, I or K had little effect, depletion of...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lund N,Milev MP,Wong R,Sanmuganantham T,Woolaway K,Chabot B,Abou Elela S,Mouland AJ,Cochrane A

    更新日期:2012-04-01 00:00:00

  • 5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy.

    abstract::(19)F NMR spectroscopy has proved to be a valuable tool to monitor functionally important conformational transitions of nucleic acids. Here, we present a systematic investigation on the application of 5-fluoro pyrimidines to probe DNA and RNA secondary structures. Oligonucleotides with the propensity to adapt secondar...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Puffer B,Kreutz C,Rieder U,Ebert MO,Konrat R,Micura R

    更新日期:2009-12-01 00:00:00

  • PDBe: Protein Data Bank in Europe.

    abstract::The Protein Data Bank in Europe (PDBe; pdbe.org) is actively involved in managing the international archive of biomacromolecular structure data as one of the partners in the Worldwide Protein Data Bank (wwPDB; wwpdb.org). PDBe also develops new tools to make structural data more widely and more easily available to the...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Velankar S,Alhroub Y,Alili A,Best C,Boutselakis HC,Caboche S,Conroy MJ,Dana JM,van Ginkel G,Golovin A,Gore SP,Gutmanas A,Haslam P,Hirshberg M,John M,Lagerstedt I,Mir S,Newman LE,Oldfield TJ,Penkett CJ,Pineda-Casti

    更新日期:2011-01-01 00:00:00

  • Rapid and efficient construction of markerless deletions in the Escherichia coli genome.

    abstract::We have developed an improved and rapid genomic engineering procedure for the construction of custom-designed microorganisms. This method, which can be performed in 2 days, permits restructuring of the Escherichia coli genome via markerless deletion of selected genomic regions. The deletion process was mediated by a s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Yu BJ,Kang KH,Lee JH,Sung BH,Kim MS,Kim SC

    更新日期:2008-08-01 00:00:00

  • Meiotic recombination protein Rec12: functional conservation, crossover homeostasis and early crossover/non-crossover decision.

    abstract::In fission yeast and other eukaryotes, Rec12 (Spo11) is thought to catalyze the formation of dsDNA breaks (DSBs) that initiate homologous recombination in meiosis. Rec12 is orthologous to the catalytic subunit of topoisomerase VI (Top6A). Guided by the crystal structure of Top6A, we engineered the rec12 locus to encod...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kan F,Davidson MK,Wahls WP

    更新日期:2011-03-01 00:00:00

  • LocDB: experimental annotations of localization for Homo sapiens and Arabidopsis thaliana.

    abstract::LocDB is a manually curated database with experimental annotations for the subcellular localizations of proteins in Homo sapiens (HS, human) and Arabidopsis thaliana (AT, thale cress). Currently, it contains entries for 19,604 UniProt proteins (HS: 13,342; AT: 6262). Each database entry contains the experimentally der...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rastogi S,Rost B

    更新日期:2011-01-01 00:00:00

  • The nucleotide sequence of the chick cytoplasmic beta-actin gene.

    abstract::The nucleotide sequence of the chick beta-actin gene was determined. The gene contains 5 introns; 4 interrupt the translated region at codons 41/42, 120/122, 267, 327/328 and a large intron occurs in the 5' untranslated region. The gene has a 97 nucleotide 5'-untranslated region and a 594 nucleotide 3'-untranslated re...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kost TA,Theodorakis N,Hughes SH

    更新日期:1983-12-10 00:00:00

  • Helix opening in deoxyribonucleic acid from a proton nuclear magnetic resonance study of imino and amino protons in d(CG)3.

    abstract::All exchangeable protons in a short DNA helix, d(CG)3 sodium salt, have been studied by proton nuclear magnetic resonance. The cytidine and guanosine amino protons have been assigned for the first time. As a function of temperature the cytidine amino protons and the imino protons behave very similarly, their relaxatio...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Fazakerley GV,van der Marel GA,van Boom JH,Guschlbauer W

    更新日期:1984-11-12 00:00:00

  • Multiple heterogeneities in the transcribed spacers of ribosomal DNA from Xenopus laevis.

    abstract::Ribosomal DNA (rDNA) from Xenopus laevis contains several heterogeneities in all three transcribed spacers, as revealed by analysis of cloned and uncloned amplified rDNA from oocytes and cloned chromosomal rDNA from erythrocytes. Heterogeneities include single base changes and length variants of one to several nucleot...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Stewart MA,Hall LM,Maden BE

    更新日期:1983-02-11 00:00:00

  • Sustained expression of miR-26a promotes chromosomal instability and tumorigenesis through regulation of CHFR.

    abstract::MicroRNA 26a (miR-26a) reduces cell viability in several cancers, indicating that miR-26a could be used as a therapeutic option in patients. We demonstrate that miR-26a not only inhibits G1-S cell cycle transition and promotes apoptosis, as previously described, but also regulates multiple cell cycle checkpoints. We s...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Castellano L,Dabrowska A,Pellegrino L,Ottaviani S,Cathcart P,Frampton AE,Krell J,Stebbing J

    更新日期:2017-05-05 00:00:00

  • KpnI families of long, interspersed repetitive DNAs in human and other primate genomes.

    abstract::KpnI restriction of DNAs from all anthropoid primates studied releases a conspicuous series of segments representing families of long, interspersed repetitive DNAs termed here the KpnI 1.2, 1.5, 1.8 and 1.9 kb families. Human KpnI 1.2 to 1.9 kb segments representative of these families were isolated and separately clo...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Shafit-Zagardo B,Maio JJ,Brown FL

    更新日期:1982-05-25 00:00:00

  • Properties of pseudo-complementary DNA substituted with weakly pairing analogs of guanine or cytosine.

    abstract::A straightforward enzymatic protocol for converting regular DNA into pseudo-complementary DNA could improve the performance of oligonucleotide microarrays by generating readily hybridizable structure-free targets. Here we screened several highly destabilizing analogs of G and C for one that could be used with 2-aminoa...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Lahoud G,Timoshchuk V,Lebedev A,Arar K,Hou YM,Gamper H

    更新日期:2008-12-01 00:00:00

  • Global transcript structure resolution of high gene density genomes through multi-platform data integration.

    abstract::Annotation of herpesvirus genomes has traditionally been undertaken through the detection of open reading frames and other genomic motifs, supplemented with sequencing of individual cDNAs. Second generation sequencing and high-density microarray studies have revealed vastly greater herpesvirus transcriptome complexity...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: O'Grady T,Wang X,Höner Zu Bentrup K,Baddoo M,Concha M,Flemington EK

    更新日期:2016-10-14 00:00:00

  • CAG*CTG repeat instability in cultured human astrocytes.

    abstract::Cells of the central nervous system (CNS) are prone to the devastating consequences of trinucleotide repeat (TNR) expansion. Some CNS cells, including astrocytes, show substantial TNR instability in affected individuals. Since astrocyte enrichment occurs in brain regions sensitive to neurodegeneration and somatic TNR ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Farrell BT,Lahue RS

    更新日期:2006-01-01 00:00:00

  • MHCPEP--a database of MHC-binding peptides: update 1995.

    abstract::MHCPEP is a curated database comprising over 6000 peptide sequences known to bind MHC molecules. Entries are compiled from published reports as well as from direct submissions of experimental data. Each entry contains peptide sequence, MHC specificity and when available, experimental method, observed activity, binding...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Brusic V,Rudy G,Kyne AP,Harrison LC

    更新日期:1996-01-01 00:00:00

  • RAD18 promotes DNA double-strand break repair during G1 phase through chromatin retention of 53BP1.

    abstract::Recruitment of RAD18 to stalled replication forks facilitates monoubiquitination of PCNA during S-phase, promoting translesion synthesis at sites of UV irradiation-induced DNA damage. In this study, we show that RAD18 is also recruited to ionizing radiation (IR)-induced sites of DNA double-strand breaks (DSBs) forming...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Watanabe K,Iwabuchi K,Sun J,Tsuji Y,Tani T,Tokunaga K,Date T,Hashimoto M,Yamaizumi M,Tateishi S

    更新日期:2009-04-01 00:00:00

  • GenBank.

    abstract::GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 9.9 trillion base pairs from over 2.1 billion nucleotide sequences for 478 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverag...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Sayers EW,Cavanaugh M,Clark K,Pruitt KD,Schoch CL,Sherry ST,Karsch-Mizrachi I

    更新日期:2021-01-08 00:00:00

  • Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation.

    abstract::In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the ...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Zhang G,Lukoszek R,Mueller-Roeber B,Ignatova Z

    更新日期:2011-04-01 00:00:00

  • Stable propagation of cosmid sized human DNA inserts in an F factor based vector.

    abstract::Instability of complex mammalian genomic DNA inserts is commonplace in cosmid libraries constructed in conventional multicopy vectors. To develop a means to construct stable libraries, we have developed a low copy number cosmid vector based on the E. coli F factor replicon (Fosmid). We have tested relative stability o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Kim UJ,Shizuya H,de Jong PJ,Birren B,Simon MI

    更新日期:1992-03-11 00:00:00

  • One short well conserved region of Alu-sequences is involved in human gene rearrangements and has homology with prokaryotic chi.

    abstract::Alu elements have repeatedly been found involved in gene rearrangements in humans. Although these elements have been suggested to stimulate gene rearrangements, sparse information is available for the possible mechanism(s) of these events. Here we present a compilation of Alu elements that have been involved in recomb...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Rüdiger NS,Gregersen N,Kielland-Brandt MC

    更新日期:1995-01-25 00:00:00

  • NMR structure of a DNA duplex containing nucleoside analog 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control.

    abstract::The three-dimensional structures of two DNA duplexes d(CATGAGTAC). d(GTACXCATG) (1) and d(CATGAGTAC).d(GTACTCATG) (2), where X represents 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole, were solved using high resolution nuclear magnetic resonance spectroscopy and restrained molecular dynamics. Good convergence was o...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Klewer DA,Hoskins A,Zhang P,Davisson VJ,Bergstrom DE,LiWang AC

    更新日期:2000-11-15 00:00:00

  • DNase I-defined chromatin configuration of the human CD3 gene cluster.

    abstract::The three CD3 genes on human chromosome 11q23 encode proteins (gamma, delta and epsilon) which form part of the antigen receptor on T lymphocytes. All three genes are clustered within 50 kb and are activated approximately contemporaneously during the early stages of T cell ontogeny. In order to pinpoint potential regu...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Tunnacliffe A

    更新日期:1990-02-11 00:00:00

  • Multi-forms of human MTH1 polypeptides produced by alternative translation initiation and single nucleotide polymorphism.

    abstract::The human MTH1 gene for 8-oxo-7,8-dihydrodeoxyguanosine triphosphatase, produces seven types (types 1, 2A, 2B, 3A, 3B, 4A and 4B) of mRNAs. The B-type mRNAs with exon 2b-2c segments have three additional in-frame AUGs in their 5' regions. We report here that these transcripts produce three forms of MTH1 polypeptides (...

    journal_title:Nucleic acids research

    pub_type: 杂志文章


    authors: Oda H,Taketomi A,Maruyama R,Itoh R,Nishioka K,Yakushiji H,Suzuki T,Sekiguchi M,Nakabeppu Y

    更新日期:1999-11-15 00:00:00