In: Journal of translational medicine, 13 (2015), Nr. 224. pp. 1-12. ISSN 1479-5876
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Abstract
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.
Document type: | Article |
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Journal or Publication Title: | Journal of translational medicine |
Volume: | 13 |
Number: | 224 |
Publisher: | BioMed Central |
Place of Publication: | London |
Date Deposited: | 24 Nov 2015 14:06 |
Date: | 2015 |
ISSN: | 1479-5876 |
Page Range: | pp. 1-12 |
Faculties / Institutes: | Medizinische Fakultät Heidelberg > Medizinische Universitäts-Klinik und Poliklinik |
DDC-classification: | 610 Medical sciences Medicine |