title: miFRame: analysis and visualization of miRNA sequencing data in neurological disorders.
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.
authors.affiliation: Chair for Clinical Computational Biology, Saarland University, Saarbrücken, Germany. c.backes@mx.uni-saarland.de.
authors.forename: Christina
authors.initials: C
authors.lastname: Backes
authors.affiliation: Internal Medicine III, Heidelberg University, Heidelberg, Germany. jan.haas@med.uni-heidelberg.de.|DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany. jan.haas@med.uni-heidelberg.de.
authors.forename: Jan
authors.initials: J
authors.lastname: Haas
authors.affiliation: Department of Human Genetics, Saarland University, Saarbrücken, Germany. p.leidinger@mx.uni-saarland.de.
authors.forename: Petra
authors.initials: P
authors.lastname: Leidinger
authors.affiliation: Internal Medicine III, Heidelberg University, Heidelberg, Germany. karen.frese@med.uni-heidelberg.de.|DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany. karen.frese@med.uni-heidelberg.de.
authors.forename: Karen
authors.initials: K
authors.lastname: Frese
authors.affiliation: Chair for Clinical Computational Biology, Saarland University, Saarbrücken, Germany. thomas.grossmann@ccb.uni-saarland.de.
authors.forename: Thomas
authors.initials: T
authors.lastname: Großmann
authors.affiliation: Neuroinflammation, Charitee, Berlin, Germany. Klemens.Ruprecht@charite.de.
authors.forename: Klemens
authors.initials: K
authors.lastname: Ruprecht
authors.affiliation: Internal Medicine III, Heidelberg University, Heidelberg, Germany. benjamin.meder@med.uni-heidelberg.de.|DZHK (German Centre for Cardiovascular Research), Heidelberg, Germany. benjamin.meder@med.uni-heidelberg.de.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Meder
authors.affiliation: Department of Human Genetics, Saarland University, Saarbrücken, Germany. hgemee@uks.eu.
authors.forename: Eckart
authors.initials: E
authors.lastname: Meese
authors.affiliation: Chair for Clinical Computational Biology, Saarland University, Saarbrücken, Germany. andreas.keller@ccb.uni-saarland.de.
authors.forename: Andreas
authors.initials: A
authors.lastname: Keller
mesh_terms: D000544:Alzheimer Disease / Q000235:genetics; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D009103:Multiple Sclerosis / Q000235:genetics; D009422:Nervous System Diseases / Q000235:genetics*; D020033:Protein Isoforms / Q000235:genetics / Q000378:metabolism; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D035683:MicroRNAs; D020033:Protein Isoforms