Methods to increase reproducibility in differential gene expression via meta-analysis.

abstract：:One of the major issues in expression profiling analysis still is to outline proper thresholds to determine differential expression, while avoiding false positives. The problem being that the variance is inversely proportional to the log of signal intensities. Aiming to solve this issue, we describe a model, expressio...

journal_title：Nucleic acids research

authors： Chuchana P,Marchand D,Nugoli M,Rodriguez C,Molinari N,Garcia-Sanz JA

更新日期：2007-01-01 00:00:00

abstract：:The HIV RT and Protease Sequence Database is an online relational database that catalogs evolutionary and drug-related human immunodeficiency virus (HIV) reverse transcriptase (RT) and protease sequence variation (http://hivdb.stanford.edu). The database contains a compilation of nearly all published HIV RT and protea...

journal_title：Nucleic acids research

authors： Shafer RW,Jung DR,Betts BJ,Xi Y,Gonzales MJ

更新日期：2000-01-01 00:00:00

abstract：:Defects in the posttranscriptional modifications of mitochondrial tRNAs have been linked to human diseases, but their pathophysiology remains elusive. In this report, we investigated the molecular mechanism underlying a deafness-associated tRNAIle 4295A>G mutation affecting a highly conserved adenosine at position 37,...

journal_title：Nucleic acids research

authors： Meng F,Zhou M,Xiao Y,Mao X,Zheng J,Lin J,Lin T,Ye Z,Cang X,Fu Y,Wang M,Guan MX

更新日期：2021-01-25 00:00:00

abstract：:OGG1 initiated base excision repair (BER) is the major pathway for repair of oxidative DNA base damage 8-oxoguanine (8-oxoG). Here, we report that RECQL4 DNA helicase, deficient in the cancer-prone and premature aging Rothmund-Thomson syndrome, physically and functionally interacts with OGG1. RECQL4 promotes catalytic...

journal_title：Nucleic acids research

authors： Duan S,Han X,Akbari M,Croteau DL,Rasmussen LJ,Bohr VA

更新日期：2020-07-09 00:00:00

abstract：:The Escherichia coli AlkB protein (EcAlkB) is a DNA repair enzyme which reverses methylation damage such as 1-methyladenine (1-meA) and 3-methylcytosine (3-meC). The mammalian AlkB homologues ALKBH2 and ALKBH3 display EcAlkB-like repair activity in vitro, but their substrate specificities are different, and ALKBH2 is ...

journal_title：Nucleic acids research

authors： Meza TJ,Moen MN,Vågbø CB,Krokan HE,Klungland A,Grini PE,Falnes PØ

更新日期：2012-08-01 00:00:00

abstract：:Small nucleolar RNAs (snoRNAs) are among the first discovered and most extensively studied group of small non-coding RNA. However, most studies focused on a small subset of snoRNAs that guide the modification of ribosomal RNA. In this study, we annotated the expression pattern of all box C/D snoRNAs in normal and canc...

journal_title：Nucleic acids research

authors： Deschamps-Francoeur G,Garneau D,Dupuis-Sandoval F,Roy A,Frappier M,Catala M,Couture S,Barbe-Marcoux M,Abou-Elela S,Scott MS

更新日期：2014-09-01 00:00:00

abstract：:PASMet (Prediction, Analysis and Simulation of Metabolic networks) is a web-based platform for proposing and verifying mathematical models to understand the dynamics of metabolism. The advantages of PASMet include user-friendliness and accessibility, which enable biologists and biochemists to easily perform mathematic...

journal_title：Nucleic acids research

authors： Sriyudthsak K,Mejia RF,Arita M,Hirai MY

更新日期：2016-07-08 00:00:00

abstract：:We have investigated the response of the filamentous fungus Aspergillus nidulans to low, non-killing, doses of the alkylating agent MNNG (N-methyl-N'-nitro-N-nitrosoguanidine). Such treatment causes a substantial induction of DNA alkyltransferase activity, with the specific activity in treated cells increasing up to o...

journal_title：Nucleic acids research

authors： Baker SM,Margison GP,Strike P

更新日期：1992-02-25 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

authors： Mohamed A,Shah AD,Chen D,Hill MM

更新日期：2019-01-08 00:00:00

abstract：:Approaches to characterize the nucleic acid-binding properties of drugs and druglike small molecules are crucial to understanding the behavior of these compounds in cellular systems. Here, we use a Small Molecule Microarray (SMM) profiling approach to identify the preferential interaction between chlorhexidine, a wide...

journal_title：Nucleic acids research

authors： Calabrese DR,Zlotkowski K,Alden S,Hewitt WM,Connelly CM,Wilson RM,Gaikwad S,Chen L,Guha R,Thomas CJ,Mock BA,Schneekloth JS Jr

更新日期：2018-04-06 00:00:00

abstract：:Hydroxylapatite chromatographies of mitochondrial and total enzymes from a rho+ yeast, or from the related rho degrees mitochondrial DNA-less mutant, show the occurrence in the mitochondrial enzyme of one Phe-, one Met-, one Leu-tRNA synthetase peak which elutes distinctly from the cytoplasmic counterpart and charges ...

journal_title：Nucleic acids research

authors： Schneller JM,Schneller C,Martin R,Stahl AJ

更新日期：1976-05-01 00:00:00

abstract：:We describe a database of macromolecular motions meant to be of general use to the structural community. The database, which is accessible on the World Wide Web with an entry point at http://bioinfo.mbb.yale.edu/MolMovDB , attempts to systematize all instances of protein and nucleic acid movement for which there is at...

journal_title：Nucleic acids research

authors： Gerstein M,Krebs W

更新日期：1998-09-15 00:00:00

abstract：:The primary function of microRNAs (miRNAs) is to maintain cell homeostasis. In cancerous tissues miRNAs' expression undergo drastic alterations. In this study, we use miRNA expression profiles from The Cancer Genome Atlas of 24 cancer types and 3 healthy tissues, collected from >8500 samples. We seek to classify the c...

journal_title：Nucleic acids research

authors： Rasnic R,Linial N,Linial M

更新日期：2017-05-19 00:00:00

abstract：:The gene, rpb2, encoding the second largest subunit, subunit 2, of RNA polymerase II has been cloned from Schizosaccharomyces pombe using the corresponding gene, RPB2, of Saccharomyces cerevisiae as a probe for cross-hybridization. We have determined the complete nucleotide sequence of rpb2, and parts of the PCR-ampli...

journal_title：Nucleic acids research

authors： Kawagishi M,Yamagishi M,Ishihama A

更新日期：1993-02-11 00:00:00

abstract：:TFIIH is a multisubunit factor essential for transcription initiation and promoter escape of RNA polymerase II and for the opening of damaged DNA double strands in nucleotide excision repair (NER). In this study, we have analyzed at which step of the transcription cycle TFIIH is essential for transcription by RNA poly...

journal_title：Nucleic acids research

authors： Assfalg R,Lebedev A,Gonzalez OG,Schelling A,Koch S,Iben S

更新日期：2012-01-01 00:00:00

abstract：:New transcripts generated by RNA polymerase II (RNAPII) are generally processed in order to form mature mRNAs. Two key processing steps include a precise cleavage within the 3' end of the pre-mRNA, and the subsequent polymerization of adenosines to produce the poly(A) tail. In yeast, these two functions are performed ...

journal_title：Nucleic acids research

authors： Guéguéniat J,Dupin AF,Stojko J,Beaurepaire L,Cianférani S,Mackereth CD,Minvielle-Sébastia L,Fribourg S

更新日期：2017-09-29 00:00:00

abstract：:Telomeres play a central role in human cancer, cardiovascular aging and possibly longevity. However, present methods to measure telomere length are fraught with shortcomings that limit their use. Here, we describe a novel method to measure the relative telomere DNA content by dot blot analysis. In each dot, the DNA co...

journal_title：Nucleic acids research

authors： Kimura M,Aviv A

更新日期：2011-07-01 00:00:00

abstract：:Expression from the K. pneumoniae nifLA promoter is oxygen sensitive and is also inhibited by the DNA gyrase inhibitor coumermycin A1 under anaerobic growth conditions. The activity of this promoter was found to be highly sensitive to changes in DNA topology in vitro. Transcription was completely dependent on negative...

journal_title：Nucleic acids research

authors： Dixon RA,Henderson NC,Austin S

更新日期：1988-11-11 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

authors： Shaban HA,Seeber A

更新日期：2020-04-17 00:00:00

abstract：:Gene promoters are enriched in guanine clusters that potentially fold into quadruplex structures. Such quadruplexes were implicated in the regulation of gene expression, plausibly by interacting with transcription factors. We showed previously that homodimers of the myogenic transcription factor MyoD bound in vitro mo...

journal_title：Nucleic acids research

authors： Shklover J,Weisman-Shomer P,Yafe A,Fry M

更新日期：2010-04-01 00:00:00

abstract：:Single-cell RNA-sequencing (scRNA-seq) enables the characterization of transcriptomic profiles at the single-cell resolution with increasingly high throughput. However, it suffers from many sources of technical noises, including insufficient mRNA molecules that lead to excess false zero values, termed dropouts. Comput...

journal_title：Nucleic acids research

authors： Xu Y,Zhang Z,You L,Liu J,Fan Z,Zhou X

更新日期：2020-09-04 00:00:00

abstract：:Fourteen P-element insertion mutants at the yellow (y) gene of D. melanogaster have been analysed by restriction mapping and DNA sequencing. The distribution of the insertion sites is nonrandom, with a preferred target site in the 5'-transcribed but non-translated leader of the gene. Transcription analysis indicates t...

journal_title：Nucleic acids research

authors： Howes G,O'Connor M,Chia W

更新日期：1988-04-11 00:00:00

abstract：:Myotonic dystrophy type 1 (DM1) is caused by the expansion of a (CTG).(CAG) repeat in the DMPK gene on chromosome 19q13.3. At least 17 neurological diseases have similar genetic mutations, the expansion of DNA repeats. In most of these disorders, the disease severity is related to the length of the repeat expansion, a...

journal_title：Nucleic acids research

authors： Hashem VI,Pytlos MJ,Klysik EA,Tsuji K,Khajavi M,Ashizawa T,Sinden RR

更新日期：2004-12-01 00:00:00

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

authors： Dougherty JD,Schmidt EF,Nakajima M,Heintz N

更新日期：2010-07-01 00:00:00

abstract：:Natural antisense transcripts are at least partially complementary to their sense transcripts. Cis-Sense/Antisense pairs (cis-SAs) have been extensively characterized and known to play diverse regulatory roles, whereas trans-Sense/Antisense pairs (trans-SAs) in animals are poorly studied. We identified long trans-SAs ...

journal_title：Nucleic acids research

authors： Li JT,Zhang Y,Kong L,Liu QR,Wei L

更新日期：2008-09-01 00:00:00

abstract：:Underlying higher order chromatin organization are Structural Maintenance of Chromosomes (SMC) complexes, large protein rings that entrap DNA. The molecular mechanism by which SMC complexes organize chromatin is as yet incompletely understood. Two prominent models posit that SMC complexes actively extrude DNA loops (l...

journal_title：Nucleic acids research

authors： Gerguri T,Fu X,Kakui Y,Khatri BS,Barrington C,Bates PA,Uhlmann F

更新日期：2021-01-12 00:00:00

abstract：:The template requirements for efficient adenovirus DNA replication were studied in vitro in a reconstituted system with cloned DNA fragments, containing the Ad2 origin region, as templates. Replication is enhanced by nuclear factor I, a cellular protein that binds specifically to the Ad2 origin. This stimulation is sh...

journal_title：Nucleic acids research

authors： de Vries E,van Driel W,Tromp M,van Boom J,van der Vliet PC

更新日期：1985-07-11 00:00:00

abstract：:Hepatitis C virus (HCV) RNA is recognized and cleaved in vitro by RNase P enzyme near the AUG start codon. Because RNase P identifies transfer RNA (tRNA) precursors, it has been proposed that HCV RNA adopts structural similarities to tRNA. Here, we present experimental evidence of RNase P sensitivity conservation in n...

journal_title：Nucleic acids research

authors： Piron M,Beguiristain N,Nadal A,Martínez-Salas E,Gómez J

更新日期：2005-03-08 00:00:00

abstract：:Bacterial transcription factors often function as DNA-binding proteins that selectively activate or repress promoters, although the biochemical mechanisms vary. In most well-understood examples, activators function by either increasing the affinity of RNA polymerase (RNAP) for the target promoter, or by increasing the...

journal_title：Nucleic acids research

authors： Gaballa A,MacLellan S,Helmann JD

更新日期：2012-04-01 00:00:00

abstract：:The abundance of Alu RNA is transiently increased by heat shock in human cell lines. This effect is specific to Alu repeats among Pol III transcribed genes, since the abundance of 7SL, 7SK, 5S and U6 RNAs is essentially unaffected by heat shock. The rapid induction of Alu expression precedes the heat shock induction o...

journal_title：Nucleic acids research

authors： Liu WM,Chu WM,Choudary PV,Schmid CW

更新日期：1995-05-25 00:00:00