title: A new algorithm for integrated analysis of miRNA-mRNA interactions based on individual classification reveals insights into bladder cancer.
abstract: BACKGROUND
  MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression. It has been proposed that miRNAs play an important role in cancer development and progression. Their ability to affect multiple gene pathways by targeting various mRNAs makes them an interesting class of regulators.
  
  
  RESULTS
  We have developed an algorithm, Classification based Analysis of Paired Expression data of RNA (CAPE RNA), which is capable of identifying altered miRNA-mRNA regulation between tissues samples that assigns interaction states to each sample without preexisting stratification of groups. The distribution of the assigned interaction states compared to given experimental groups is used to assess the quality of a predicted interaction. We demonstrate the applicability of our approach by analyzing urothelial carcinoma and normal bladder tissue samples derived from 24 patients. Using our approach, normal and tumor tissue samples as well as different stages of tumor progression were successfully stratified. Also, our results suggest interesting differentially regulated miRNA-mRNA interactions associated with bladder tumor progression.
  
  
  CONCLUSIONS
  The need for tools that allow an integrative analysis of microRNA and mRNA expression data has been addressed. With this study, we provide an algorithm that emphasizes on the distribution of samples to rank differentially regulated miRNA-mRNA interactions. This is a new point of view compared to current approaches. From bootstrapping analysis, our ranking yields features that build strong classifiers. Further analysis reveals genes identified as differentially regulated by miRNAs to be enriched in cancer pathways, thus suggesting biologically interesting interactions.
authors.affiliation: Center for Bioinformatics, University of Hamburg, Hamburg, Germany.
authors.forename: Nikolai
authors.initials: N
authors.lastname: Hecker
authors.forename: Carsten
authors.initials: C
authors.lastname: Stephan
authors.forename: Hans-Joachim
authors.initials: HJ
authors.lastname: Mollenkopf
authors.forename: Klaus
authors.initials: K
authors.lastname: Jung
authors.forename: Robert
authors.initials: R
authors.lastname: Preissner
authors.forename: Hellmuth-A
authors.initials: HA
authors.lastname: Meyer
mesh_terms: D000368:Aged; D000369:Aged, 80 and over; D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D005260:Female; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D008297:Male; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D008875:Middle Aged; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism; D012680:Sensitivity and Specificity; D015398:Signal Transduction; D001749:Urinary Bladder Neoplasms / Q000235:genetics* / Q000378:metabolism / Q000473:pathology
chemical_list: D035683:MicroRNAs; D012333:RNA, Messenger