miFRame: analysis and visualization of miRNA sequencing data in neurological disorders

Journal of Translational Medicine

Andreas Keller³  Eckart Meese¹  Benjamin Meder²  Klemens Ruprecht⁴  Thomas Großmann³  Karen Frese²  Petra Leidinger¹  Jan Haas²  Christina Backes³ 

[1] Department of Human Genetics, Saarland University, Saarbrücken, Germany;DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany;Chair for Clinical Computational Biology, Saarland University, Saarbrücken, Germany;Neuroinflammation, Charitee, Berlin, Germany

关键词: Biomarkers;    Web service;    Alzheimer;    miRNA;   

Others  :  1221464
DOI  :  10.1186/s12967-015-0594-x

 received in 2015-02-22, accepted in 2015-07-02,  发布年份 2015

【 摘 要 】

Background

While in the past decades nucleic acid analysis has been predominantly carried out using quantitative low- and high-throughput approaches such as qRT-PCR and microarray technology, next-generation sequencing (NGS) with its single base resolution is now frequently applied in DNA and RNA testing. Especially for small non-coding RNAs such as microRNAs there is a need for analysis and visualization tools that facilitate interpretation of the results also for clinicians.

Methods

We developed miFRame, which supports the analysis of human small RNA NGS data. Our tool carries out different data analyses for known as well as predicted novel mature microRNAs from known precursors and presents the results in a well interpretable manner. Analyses include among others expression analysis of precursors and mature miRNAs, detection of novel precursors and detection of potential iso-microRNAs. Aggregation of results from different users moreover allows for evaluation whether remarkable results, such as novel mature miRNAs, are indeed specific for the respective experimental set-up or are frequently detected across a broad range of experiments.

Results

We demonstrate the capabilities of miFRame, which is freely available at http://www.ccb.uni-saarland.de/miframe on two studies, circulating biomarker screening for Multiple Sclerosis (cohort includes clinically isolated syndrome, relapse remitting MS, matched controls) as well as Alzheimer Disease (cohort includes Alzheimer Disease, Mild Cognitive Impairment, matched controls). Here, our tool allowed for an improved biomarker discovery by identifying likely false positive marker candidates.

【 授权许可】

   
2015 Backes et al.

【 图 表 】

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