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  • Expression
  • Expression quantitative trait loci in long non-coding RNA ZNRD1-AS1 influence both HBV infection and hepatocellular carcinoma development. (nih.gov)
  • rRNA
  • and that every sequence of bases in rRNA has information encoding more than one of these functions in addition to acting as a structural component of the ribosome. (theleagueofreason.co.uk)
  • 2017. Effects of Increasing the Affinity of CarD for RNA Polymerase on Mycobacterium tuberculosis Growth, rRNA Transcription, and Virulence . (rutgers.edu)
  • For example, miRNAs regulate protein coding gene expression by binding to 3' UTRs, small nucleolar RNAs guide post-transcriptional modifications by binding to rRNA, U4 spliceosomal RNA and U6 spliceosomal RNA bind to each other forming part of the spliceosome and many small bacterial RNAs regulate gene expression by antisense interactions E.g. (wikipedia.org)
  • novel
  • Although the small sample size prevents us from drawing definite conclusions, we observed promising novel co-expression networks for IAs: WCGNA analysis showed down-regulation of two transcript modules associated with ruptured IA status (r=-0.78, p=0.008 and r=-0.77, p=0.009), and up-regulation of two modules associated with aneurysm size (r=0.86, p=0.002 and r=0.9, p=4e-04), respectively. (ahajournals.org)
  • In recent years, next generation sequencing technology has already become available to screen known and novel gene fusion events on a genome wide scale. (wikipedia.org)
  • genomic
  • Badger & Olsen use the BLASTN program [ 17 ] to locate genomic regions with significant sequence similarity between two related bacterial species. (biomedcentral.com)
  • Integrated genomic and transcriptomic analysis of human brain metastases identifies alterations of potential clinical significance," Journal of Pathology , vol. 237, no. 3, pp. 363-378, 2015. (hindawi.com)
  • gene expression
  • Only on a single-cell level, can you eliminate the biological noise that is inherent to standard gene expression analysis - providing you the insights needed for a deeper understanding of transcription dynamics. (qiagen.com)
  • We utilized weighted gene co-expression network analysis (WGCNA) to identify gene expression network modules associated with IA size and rupture. (ahajournals.org)
  • Prior to RNA-Seq, gene expression studies were done with hybridization-based microarrays. (wikipedia.org)
  • These progressed from Sanger sequencing of Expressed Sequence Tag libraries, to chemical tag-based methods (e.g., serial analysis of gene expression), and finally to the current technology, next-gen sequencing of cDNA (notably RNA-Seq). (wikipedia.org)
  • A variety of parameters are considered when designing and conducting RNA-Seq experiments: Tissue specificity: Gene expression varies within and between tissues, and RNA-Seq measures this mix of cell types. (wikipedia.org)
  • functional
  • Maizel and coworkers [ 13 - 15 ] had hypothesized that biologically functional RNA structures may have more stable predicted secondary structures than would be expected for a random sequence of the same base composition. (biomedcentral.com)
  • Geometry-dependent functional changes in iPSC-derived cardiomyocytes probed by functional imaging and RNA sequencing. (ucdenver.edu)
  • RBPs curated from different experimental studies are reported with their annotation, tissue-wide RNA and protein expression levels, evolutionary conservation, disease associations, protein-protein interactions, microRNA predictions, their known RNA recognition sequence motifs as well as predicted binding targets and associated functional themes, providing a one stop portal for understanding the expression, evolutionary trajectories and disease dynamics of RBPs in the context of post-transcriptional regulatory networks. (omictools.com)
  • Highly conserved DNA sequences are thought to have functional value, although the role for many highly conserved non-coding DNA sequences is poorly understood. (wikipedia.org)
  • Many functional sequences are also modular, containing regions which may be subject to independent selection pressures, such as protein domains. (wikipedia.org)
  • Interactions
  • 2016. Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection. . (rutgers.edu)
  • alignments
  • We formalize this intuition using three probabilistic "pair-grammars": a pair stochastic context free grammar modeling alignments constrained by structural RNA evolution, a pair hidden Markov model modeling alignments constrained by coding sequence evolution, and a pair hidden Markov model modeling a null hypothesis of position-independent evolution. (biomedcentral.com)
  • A common analysis workflow of RNA-sequencing (RNA-seq) data consists of mapping the sequencing reads to a reference genome, followed by the transcript assembly and quantification based on these alignments. (helsinki.fi)
  • The evaluated approaches included aligning the long reads to a graph created from short read alignments instead of the reference genome, which led to our final contribution: extending a co-linear chaining algorithm from between two sequences to between a sequence and a directed acyclic graph. (helsinki.fi)
  • Homology search tools may take an individual nucleic acid or protein sequence as input, or use statistical models generated from multiple sequence alignments of known related sequences. (wikipedia.org)
  • Producing multiple sequence alignments (MSA) of these families can provide insight into their structure and function, similar to the case of protein families. (wikipedia.org)
  • Each family in the database is represented by two multiple sequence alignments in Stockholm format and a SCFG. (wikipedia.org)
  • tRNA
  • Transfer-messenger RNA (abbreviated tmRNA, also known as 10Sa RNA and by its genetic name SsrA) is a bacterial RNA molecule with dual tRNA-like and messenger RNA-like properties. (wikipedia.org)
  • The presence of pseudouridine in the mixed 10S RNA hinted that tmRNA has modified bases found also in tRNA. (wikipedia.org)
  • The similarity at the 3' end of tmRNA to the T stem-loop of tRNA was first recognized upon sequencing ssrA from Mycobacterium tuberculosis. (wikipedia.org)
  • Subsequent sequence comparison revealed the full tRNA-like domain (TLD) formed by the 5' and 3' ends of tmRNA, including the acceptor stem with elements like those in alanine tRNA that promote its aminoacylation by alanine-tRNA ligase. (wikipedia.org)
  • bacterial
  • In other bacterial species, a permuted ssrA gene produces a two-piece tmRNA in which two separate RNA chains are joined by base-pairing. (wikipedia.org)
  • genetic
  • I used to think that any knowledge of how that RNA world looked and what kinds of genetic machinery was contained within it, was forever obscured by the erasing nature of the accumulating mutations of time and the gradual replacement and loss of these primordially essential components. (theleagueofreason.co.uk)
  • The extent to which a sequence is conserved can be affected by varying selection pressures, its robustness to mutation, population size and genetic drift. (wikipedia.org)
  • citation needed] In coding sequences, the nucleic acid and amino acid sequence may be conserved to different extents, as the degeneracy of the genetic code means that synonymous mutations in a coding sequence do not affect the amino acid sequence of its protein product. (wikipedia.org)
  • cDNA
  • The general steps to prepare a complementary DNA (cDNA) library for sequencing are described below, but often vary between platforms. (wikipedia.org)
  • cDNA synthesis: DNA sequencing technology is more mature, so the RNA is reverse transcribed to cDNA. (wikipedia.org)
  • The cDNA for each experiment can be indexed with a hexamer or octamer barcode, so that these experiments can be pooled into a single lane for multiplexed sequencing. (wikipedia.org)
  • bind
  • InvR has been shown to bind the RNA chaperone Hfq in vitro and Hfq is required for in vivo stability. (wikipedia.org)
  • downstream
  • Since scRNA-seq requires amplification of a low amount of endogenous cellular RNA, leading to substantial technical noise in the dataset, downstream data filtering and analysis require special care. (springer.com)
  • We illustrate the implications of these issues on downstream analysis, such as somatic mutation and fusion calling and differential expression. (aacrjournals.org)
  • Our analysis has characterized the technical features of the different library preparations, providing a necessary understanding of the costs and benefits of each method and the potential effects on the downstream analyses. (aacrjournals.org)
  • The a1, b1 site is upstream of the c4 RNA, while the a2, b2 site is immediately downstream of it. (wikipedia.org)
  • small
  • Sequence analysis of the small RNA segment of guinea pig-passaged Pichinde virus variants. (ajtmh.org)
  • Catara, Antonino 2015-10-01 00:00:00 Two representative isolates of a citrus tristeza virus population in Sicily, SG29 (aggressive) and Bau282 (mild), were sequenced via viral small RNAs (vsRNA) produced in budlings of sweet orange grafted on sour orange. (deepdyve.com)
  • In RNA-Seq, mRNAs are split into small fragments, filtered by length, and sequenced. (coursera.org)
  • Fragmentation is followed by size selection, where either small sequences are removed or a tight range of sequence lengths are selected. (wikipedia.org)
  • The single sequence methods mentioned above have a difficult job detecting a small sample of reasonable secondary structures from a large space of possible structures. (wikipedia.org)
  • mutations
  • A conserved coding region tends to show a pattern of synonymous substitutions, whereas a conserved structural RNA tends to show a pattern of compensatory mutations consistent with some base-paired secondary structure. (biomedcentral.com)
  • Over many generations, nucleic acid sequences in the genome of an evolutionary lineage can gradually change over time due to random mutations and deletions. (wikipedia.org)
  • The codon usage bias in some organisms may restrict the types of synonymous mutations in a sequence. (wikipedia.org)
  • degradation
  • The tmRNA is remarkably versatile: it recycles the stalled ribosome, adds a proteolysis-inducing tag to the unfinished polypeptide, and facilitates the degradation of the aberrant messenger RNA. (wikipedia.org)
  • The amount of RNA degradation is checked with gel and capillary electrophoresis and is used to assign an RNA integrity number to the sample. (wikipedia.org)
  • structures
  • This suggests that tmRNA folding outside the TLD can be important, yet the pseudoknot region lacks conserved residues and pseudoknots are among the first structures to be lost as ssrA sequences diverge in plastid and endosymbiont lineages. (wikipedia.org)
  • Probabilistic context free grammars (PCFGs) have been applied in probabilistic modeling of RNA structures almost 40 years after they were introduced in computational linguistics. (wikipedia.org)
  • stability
  • Within a sequence, amino acids that are important for folding, structural stability, or that form a binding site may be more highly conserved. (wikipedia.org)
  • transcriptomics
  • In summary, we have described a RNA-seq analysis platform that provides a varied set of library preparations and analytical components for large-scale clinical or research transcriptomics. (aacrjournals.org)
  • Because of these technical issues, transcriptomics transitioned to sequencing-based methods. (wikipedia.org)
  • optimal
  • While there are many resources readily available to effectively perform RNA-seq experiments, optimal protocols and analysis tools for the cancer domain remain to be developed. (aacrjournals.org)
  • reads
  • It is a curious fact to consider, that the ribosome is a large, mostly RNA-based molecular machine that 'reads' RNA, as one would expect a putative primordial self-replicating RNA or RNA-polymerase would do. (theleagueofreason.co.uk)
  • cellular
  • Therefore, we also briefly describe in-house state-of-the-art data analysis algorithms developed to identify cellular subpopulations including rare cell types as well as to derive lineage trees by ordering the identified subpopulations of cells along the inferred differentiation trajectories. (springer.com)
  • The cellular RNA is selected based on the desired size range. (wikipedia.org)