1,720,986 research outputs found
AURA: Atlas of UTR Regulatory Activity
No full textSUMMARY:
The Atlas of UTR Regulatory Activity (AURA) is a manually curated and comprehensive catalog of human mRNA untranslated regions (UTRs) and UTR regulatory annotations. Through its intuitive web interface, it provides full access to a wealth of information on UTRs that integrates phylogenetic conservation, RNA sequence and structure data, single nucleotide variation, gene expression and gene functional descriptions from literature and specialized databases.
AVAILABILITY:
http://aura.science.unitn.it
CONTACT:
[email protected]; [email protected]
SUPPLEMENTARY INFORMATION:
Supplementary data are available at Bioinformatics online
AURA 2: Empowering the discovery of post-transcriptional networks
No full textPost-transcriptional regulation (PTR) of gene expression is now recognized as a major determinant of cell phenotypes. The recent availability of methods to map protein-RNA interactions in entire transcriptomes such as RIP, CLIP and their variants, together with global polysomal and ribosome profiling techniques, are driving the exponential accumulation of vast amounts of data on mRNA contacts in cells, and of corresponding predictions of PTR events. However, this exceptional quantity of information cannot be exploited at its best to reconstruct potential PTR networks, as it still lies scattered throughout several databases and in isolated reports of single interactions. To address this issue, we developed the second and vastly enhanced version of the Atlas of UTR Regulatory Activity (AURA 2), a meta-database centered on mapping interaction of trans-factors with human and mouse UTRs. AURA 2 includes experimentally demonstrated binding sites for RBPs, ncRNAs, thousands of cis-elements, variations, RNA epigenetics data, and more. Its user-friendly interface offers various data-mining features including co-regulation search, network generation, and regulatory enrichment testing. Gene expression profiles for many tissues and cell lines can be also combined with these analyses to display only the interactions possible in the system under study. AURA 2 aims at becoming a valuable toolbox for PTR studies and at tracing the road for how PTR network-building tools should be designed. AURA 2 is available at http://aura.science.unitn.it
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Computational and experimental detection of uncoupling between transcriptome and translatome changes of gene expression
No full textTranscriptome analysis by total mRNA profiling provides a measurement of the degree of variation for the amount of each single mRNA species after a physiological or pathological transition of cell state. It has become a general notion that variations in protein levels do not necessarily correlate with variations in total mRNA levels, for the presence of post-transcriptional controls which influence the fate of cytoplasmic mRNAs and affect their translational fitness. Nevertheless, the extent of this phenomenon and the rules, if any, governing it are still generally unknown.
To address this issue we took advantage of a number of studies performed using polysomal mRNA profiling in combination with classical total mRNA profiling in different mammalian and yeast systems. A normalization of the raw data coming from these datasets and a statistical meta-analysis aimed at maximizing uniformity in data processing have been performed. From the comparison of the results an extensive uncoupling between transcriptome and translatome variations of mRNA levels emerges, measured by a significant difference between steady state and polysomal fold changes induced by a cellular physiological or pathological transition.
It seems clear that virtually the majority of significant changes in cytoplasmic mRNA steady-state levels are subjected to a further elaboration by a post-transcriptional decision program, leading either to a widespread buffering of the cytoplasmic changes which transfers only a small fraction of them to translation, either to the creation of new changes which cannot be detected at the transcriptional level, yet capable of heavily influencing protein synthesis rates.
An explanatory model characterized by a cytoplasmic mRNA storage compartments is proposed and the involvement of P-bodies and the miRNA pathway in post-transcriptional reprogramming of gene expression has been experimentally tested in the biological model of EGF induction, in order to explain how a change in translational fitness can counteract or magnify a parallel change in citoplasmic mRNA availability. To investigate the role of specific cellular mechanism in generating uncoupling between transcriptome and translatome changes, the experimental model has been altered through silencing of three key genes involved in post-transcriptional regulation pathways: 4E-T, Xrn1 and Dicer
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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