Dataset Information

MiRBaseMiner, a tool for investigating miRBase content.

ABSTRACT: microRNAs are small non-coding RNA molecules playing a central role in gene regulation. miRBase is the standard reference source for analysis and interpretation of experimental studies. However, the richness and complexity of the annotation is often underappreciated by users. Moreover, even for experienced users, the size of the resource can make it difficult to explore annotation to determine features such as species coverage, the impact of specific characteristics and changes between successive releases. A further consideration is that each new miRBase release contains entries that have had limited review and which may subsequently be removed in a future release to ensure the quality of annotation. To aid the miRBase user, we developed a software tool, miRBaseMiner, for investigating miRBase annotation and generating custom annotation sets. We apply the tool to characterize each release from v9.2 to v22 to examine how annotation has changed across releases and highlight some of the annotation features that users should keep in mind when using for miRBase for data analysis. These include: (1) entries with identical or very similar sequences; (2) entries with multiple annotated genome locations; (3) hairpin precursor entries with extremely low-estimated minimum free energy; (4) entries possessing reverse complementary; (5) entries with 3' poly(A) ends. As each of these factors can impact the identification of dysregulated features and subsequent clinical or biological conclusions, miRBaseMiner is a valuable resource for any user using miRBase as a reference source.

SUBMITTER: Zhong X

PROVIDER: S-EPMC6779376 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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miRBaseMiner, a tool for investigating miRBase content.

Zhong Xiangfu X Heinicke Fatima F Rayner Simon S

RNA biology 20190812 11

microRNAs are small non-coding RNA molecules playing a central role in gene regulation. miRBase is the standard reference source for analysis and interpretation of experimental studies. However, the richness and complexity of the annotation is often underappreciated by users. Moreover, even for experienced users, the size of the resource can make it difficult to explore annotation to determine features such as species coverage, the impact of specific characteristics and changes between successiv ...[more]

PMID: 31251108

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Project description:BackgroundDespite the increasing number of mobile health applications, the validity of their content is understudied. The objective of this study was to rate the content of HIV/AIDS-related mobile applications and to determine the extent to which evidence-based medicine is being incorporated into their content using a new tool called the Evidence-based content rating tool of mobile health applications (EBCRT-mHealth).MethodsAll available HIV/AIDS-related applications in Iran from Cafe Bazaar and Google Play Store were evaluated. This study was first conducted in 2018, then after almost two years in 2021 was done again. In this study, researchers developed the EBCRT-mHealth tool to rate the content of applications based on the evidence-based medicine pyramid. Its reliability was calculated (α = 0.78), and five specialists confirmed its validity. Two reviewers independently reviewed all HIV/AIDS applications directly downloaded and installed from the Google Play Store and Cafe Bazaar.ResultsOut of 980 retrieved applications, in 2018, 85, and in 2021, 78 applications were included in the study. Only in 17 (28%) out of the 60 in 2018, and 25 (51%) in 2021 Google Play store applications the source of content information was mentioned. All Cafe Bazaar mobile applications mentioned the source of information. The mean rating of all application content in 2018 was 2.38 (SD = 0.74), and in 2021 was 2.90 (SD = 1.35) out of 5. The mean rating of the content of Cafe Bazaar applications in 2018 was 2.10 (SD = 0.49), and in 2021 was 1.94 (SD = 0.29). The mean content rating of Google Play store applications in 2018 was 2.50 (SD = 0.80) and in 2021 was 3.86 (SD = 1.18).ConclusionAfter two years, the rating of the content of HIV/AIDS-related applications available in Iran that existed in Cafe Bazaar decreased from "poor" to "inappropriate". Also, the content score of the Google Play Store applications increased from "poor" to "good". It is critical to ensure the credibility of the sources used in developing their content and removing applications with inappropriate and unreliable content from the App Stores. Also, mobile health application developers should use the highest quality information in their applications.

Project description:BackgroundThe collection and analysis of Atomic Force Microscopy force curves is a well-established procedure to obtain high-resolution information of non-topographic data from any kind of sample, including biological specimens. In particular, these analyses are commonly employed to study elasticity, stiffness or adhesion properties of the samples. Furthermore, the collection of several force curves over an extended area of the specimens allows reconstructing maps, called force volume maps, of the spatial distribution of the mechanical properties. Coupling these maps with the conventional high-resolution topographic reconstruction of the sample's surface, provides a deeper insight on the sample composition from the structural and nanomechanical point of view.ResultsIn this paper we present the open source software package FC_analysis that automatically analyses single force curves or entire force volume maps to yield the corresponding elasticity and deformability images. The principal characteristic of the FC_analysis is a large adaptability to the various experimental setups and to different analysis methodologies. For instance, the user can provide custom values for the detector sensitivity, scanner-z sensitivity, cantilever's elastic constant and map's acquisition modality and can choose between different analysis methodologies. Furthermore, the software allows the optimization of the fitting parameters and gives direct control on each step of the analysis procedure. Notably, to overcome a limitation common to many other analysis programs, FC_analysis can be applied to a rectangular portion of the image, allowing the analysis of inhomogeneous samples. Finally, the software allows reconstructing a Young's modulus map at different penetration depths, enabling the use of modern investigation tools such as the force tomography.ConclusionsThe FC_analysis software aims to become a useful tool for the analysis of force curves maps collected using custom or commercial Atomic Force Microscopes, and is especially useful in those cases for which the producer doesn't release a dedicated software.

Dataset Information

MiRBaseMiner, a tool for investigating miRBase content.

Publications

miRBaseMiner, a tool for investigating miRBase content.

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