Relevant bibliographies by topics / Motif significance analysis

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Academic literature on the topic 'Motif significance analysis'

Author: Grafiati
Published: 20 February 2023

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Journal articles on the topic "Motif significance analysis"

1

Ng, P., and U. Keich. "GIMSAN: a Gibbs motif finder with significance analysis." Bioinformatics 24, no. 19 (2008): 2256–57. http://dx.doi.org/10.1093/bioinformatics/btn408.

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2

Zhong, Xuehua, Neocles Leontis, Shuiming Qian, et al. "Tertiary Structural and Functional Analyses of a Viroid RNA Motif by Isostericity Matrix and Mutagenesis Reveal Its Essential Role in Replication." Journal of Virology 80, no. 17 (2006): 8566–81. http://dx.doi.org/10.1128/jvi.00837-06.

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ABSTRACT RNA-templated RNA replication is essential for viral or viroid infection, as well as for regulation of cellular gene expression. Specific RNA motifs likely regulate various aspects of this replication. Viroids of the Pospiviroidae family, as represented by the Potato spindle tuber viroid (PSTVd), replicate in the nucleus by utilizing DNA-dependent RNA polymerase II. We investigated the role of the loop E (sarcin/ricin) motif of the PSTVd genomic RNA in replication. A tertiary-structural model of this motif, inferred by comparative sequence analysis and comparison with nuclear magnetic resonance and X-ray crystal structures of loop E motifs in other RNAs, is presented in which core non-Watson-Crick base pairs are precisely specified. Isostericity matrix analysis of these base pairs showed that the model accounts for the reported natural sequence variations and viable experimental mutations in loop E motifs of PSTVd and other viroids. Furthermore, isostericity matrix analysis allowed us to design disruptive, as well as compensatory, mutations of PSTVd loop E. Functional analyses of such mutants by in vitro and in vivo experiments demonstrated that loop E structural integrity is crucial for replication, specifically during transcription. Our results suggest that the PSTVd loop E motif exists and functions in vivo and provide loss-of-function genetic evidence for the essential role of a viroid RNA three-dimensional motif in rolling-circle replication. The use of isostericity matrix analysis of non-Watson-Crick base pairing to rationalize mutagenesis of tertiary motifs and systematic in vitro and in vivo functional assays of mutants offers a novel, comprehensive approach to elucidate the tertiary-structure-function relationships for RNA motifs of general biological significance.
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3

Kulyyassov, Arman, and Ruslan Kalendar. "In Silico Estimation of the Abundance and Phylogenetic Significance of the Composite Oct4-Sox2 Binding Motifs within a Wide Range of Species." Data 5, no. 4 (2020): 111. http://dx.doi.org/10.3390/data5040111.

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High-throughput sequencing technologies have greatly accelerated the progress of genomics, transcriptomics, and metagenomics. Currently, a large amount of genomic data from various organisms is being generated, the volume of which is increasing every year. Therefore, the development of methods that allow the rapid search and analysis of DNA sequences is urgent. Here, we present a novel motif-based high-throughput sequence scoring method that generates genome information. We found and identified Utf1-like, Fgf4-like, and Hoxb1-like motifs, which are cis-regulatory elements for the pluripotency transcription factors Sox2 and Oct4 within the genomes of different eukaryotic organisms. The genome-wide analysis of these motifs was performed to understand the impact of their diversification on mammalian genome evolution. Utf1-like, Fgf4-like, and Hoxb1-like motif diversity was evaluated across genomes from multiple species.
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4

Xie, Wen-Jie, Rui-Qi Han, and Wei-Xing Zhou. "Time series classification based on triadic time series motifs." International Journal of Modern Physics B 33, no. 21 (2019): 1950237. http://dx.doi.org/10.1142/s0217979219502370.

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It is of great significance to identify the characteristics of time series to quantify their similarity and classify different classes of time series. We define six types of triadic time-series motifs and investigate the motif occurrence profiles extracted from the time series. Based on triadic time series motif profiles, we further propose to estimate the similarity coefficients between different time series and classify these time series with high accuracy. We validate the method with time series generated from nonlinear dynamic systems (logistic map, chaotic logistic map, chaotic Henon map, chaotic Ikeda map, hyperchaotic generalized Henon map and hyperchaotic folded-tower map) and retrieved from the UCR Time Series Classification Archive. Our analysis shows that the proposed triadic time series motif analysis performs better than the classic dynamic time wrapping method in classifying time series for certain datasets investigated in this work.
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5

Bernstein, Kara A., Sander Granneman, Alicia V. Lee, Swarnameenakshi Manickam, and Susan J. Baserga. "Comprehensive Mutational Analysis of Yeast DEXD/H Box RNA Helicases Involved in Large Ribosomal Subunit Biogenesis." Molecular and Cellular Biology 26, no. 4 (2006): 1195–208. http://dx.doi.org/10.1128/mcb.26.4.1195-1208.2006.

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ABSTRACT DEXD/H box putative RNA helicases are required for pre-rRNA processing in Saccharomyces cerevisiae, although their exact roles and substrates are unknown. To characterize the significance of the conserved motifs for helicase function, a series of five mutations were created in each of the eight essential RNA helicases (Has1, Dbp6, Dbp10, Mak5, Mtr4, Drs1, Spb4, and Dbp9) involved in 60S ribosomal subunit biogenesis. Each mutant helicase was screened for the ability to confer dominant negative growth defects and for functional complementation. Different mutations showed different degrees of growth inhibition among the helicases, suggesting that the conserved regions do not function identically in vivo. Mutations in motif I and motif II (the DEXD/H box) often conferred dominant negative growth defects, indicating that these mutations do not interfere with substrate binding. In addition, mutations in the putative unwinding domains (motif III) demonstrated that conserved amino acids are often not essential for function. Northern analysis of steady-state RNA from strains expressing mutant helicases showed that the dominant negative mutations also altered pre-rRNA processing. Coimmunoprecipitation experiments indicated that some RNA helicases associated with each other. In addition, we found that yeasts disrupted in expression of the two nonessential RNA helicases, Dbp3 and Dbp7, grew worse than when either one alone was disrupted.
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6

Gazit, E. "Global analysis of tandem aromatic octapeptide repeats: The significance of the aromatic-glycine motif." Bioinformatics 18, no. 6 (2002): 880–83. http://dx.doi.org/10.1093/bioinformatics/18.6.880.

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7

Dries, Angelyn. "The Hero-Martyr Myth in United States Catholic Foreign Mission Literature, 1893–1925." Missiology: An International Review 19, no. 3 (1991): 305–14. http://dx.doi.org/10.1177/009182969101900304.

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A contextual analysis of the mission literature of several United States Catholic groups engaged in mission outreach to other countries shows extensive use of a hero-martyr motif. Four elements of this motif are examined for their significance for the missionaries themselves and for the advantage this motif carried to persuade United States Catholics to support efforts toward missions abroad at a time when the country was considered, at least by Roman authorities, to be “mission territory.”
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8

Pillon, Monica C., Kevin H. Goslen, Jacob Gordon, Melissa L. Wells, Jason G. Williams, and Robin E. Stanley. "It takes two (Las1 HEPN endoribonuclease domains) to cut RNA correctly." Journal of Biological Chemistry 295, no. 18 (2020): 5857–70. http://dx.doi.org/10.1074/jbc.ra119.011193.

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The ribosome biogenesis factor Las1 is an essential endoribonuclease that is well-conserved across eukaryotes and a newly established member of the higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domain-containing nuclease family. HEPN nucleases participate in diverse RNA cleavage pathways and share a short HEPN nuclease motif (RφXXXH) important for RNA cleavage. Most HEPN nucleases participate in stress-activated RNA cleavage pathways; Las1 plays a fundamental role in processing pre-rRNA. Underscoring the significance of Las1 function in the cell, mutations in the human LAS1L (LAS1-like) gene have been associated with neurological dysfunction. Two juxtaposed HEPN nuclease motifs create Las1's composite nuclease active site, but the roles of the individual HEPN motif residues are poorly defined. Here using a combination of in vivo experiments in Saccharomyces cerevisiae and in vitro assays, we show that both HEPN nuclease motifs are required for Las1 nuclease activity and fidelity. Through in-depth sequence analysis and systematic mutagenesis, we determined the consensus HEPN motif in the Las1 subfamily and uncovered its canonical and specialized elements. Using reconstituted Las1 HEPN-HEPN′ chimeras, we defined the molecular requirements for RNA cleavage. Intriguingly, both copies of the Las1 HEPN motif were important for nuclease function, revealing that both HEPN motifs participate in coordinating the RNA within the Las1 active site. We also established that conformational flexibility of the two HEPN domains is important for proper nuclease function. The results of our work reveal critical information about how dual HEPN domains come together to drive Las1-mediated RNA cleavage.
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9

Friend, Lindzy D., Dulari D. Shah, Christine Deppong, et al. "A dose-dependent requirement for the proline motif of CD28 in cellular and humoral immunity revealed by a targeted knockin mutant." Journal of Experimental Medicine 203, no. 9 (2006): 2121–33. http://dx.doi.org/10.1084/jem.20052230.

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Activation of naive T cells requires the integration of signals through the antigen receptor and CD28. Although there is agreement on the importance of CD28, there remains controversy on the mechanism by which CD28 regulates T cell function. We have generated a gene-targeted knockin mouse expressing a mutation in the C-terminal proline-rich region of the cytoplasmic tail of CD28. Our analysis conclusively showed that this motif is essential for CD28-dependent regulation of interleukin 2 secretion and proliferation. In vivo analysis revealed that mutation of this motif-dissociated CD28-dependent regulation of cellular and humoral responses in an allergic airway inflammation model. Furthermore, we find an important gene dosage effect on the phenotype of the mutation and provide a mechanistic explanation for the conflicting data on the significance of this motif in CD28 function.
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10

Ng, P., N. Nagarajan, N. Jones, and U. Keich. "Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone." Bioinformatics 22, no. 14 (2006): e393-e401. http://dx.doi.org/10.1093/bioinformatics/btl245.

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