title: Comparison of microarray platforms for measuring differential microRNA expression in paired normal/cancer colon tissues.
abstract: BACKGROUND
  Microarray technology applied to microRNA (miRNA) profiling is a promising tool in many research fields; nevertheless, independent studies characterizing the same pathology have often reported poorly overlapping results. miRNA analysis methods have only recently been systematically compared but only in few cases using clinical samples.
  
  
  RESULTS
  We investigated the inter-platform reproducibility of four miRNA microarray platforms (Agilent, Exiqon, Illumina, and Miltenyi), comparing nine paired tumor/normal colon tissues. The most concordant and selected discordant miRNAs were further studied by quantitative RT-PCR. Globally, a poor overlap among differentially expressed miRNAs identified by each platform was found. Nevertheless, for eight miRNAs high agreement in differential expression among the four platforms and comparability to qRT-PCR was observed. Furthermore, most of the miRNA sets identified by each platform are coherently enriched in data from the other platforms and the great majority of colon cancer associated miRNA sets derived from the literature were validated in our data, independently from the platform. Computational integration of miRNA and gene expression profiles suggested that anti-correlated predicted target genes of differentially expressed miRNAs are commonly enriched in cancer-related pathways and in genes involved in glycolysis and nutrient transport.
  
  
  CONCLUSIONS
  Technical and analytical challenges in measuring miRNAs still remain and further research is required in order to increase consistency between different microarray-based methodologies. However, a better inter-platform agreement was found by looking at miRNA sets instead of single miRNAs and through a miRNAs - gene expression integration approach.
authors.affiliation: Functional Genomics Core Facility, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy.
authors.forename: Maurizio
authors.initials: M
authors.lastname: Callari
authors.forename: Matteo
authors.initials: M
authors.lastname: Dugo
authors.forename: Valeria
authors.initials: V
authors.lastname: Musella
authors.forename: Edoardo
authors.initials: E
authors.lastname: Marchesi
authors.forename: Giovanna
authors.initials: G
authors.lastname: Chiorino
authors.forename: Maurizia Mello
authors.initials: MM
authors.lastname: Grand
authors.forename: Marco Alessandro
authors.initials: MA
authors.lastname: Pierotti
authors.forename: Maria Grazia
authors.initials: MG
authors.lastname: Daidone
authors.forename: Silvana
authors.initials: S
authors.lastname: Canevari
authors.forename: Loris
authors.initials: L
authors.lastname: De Cecco
mesh_terms: D016000:Cluster Analysis; D003106:Colon / Q000378:metabolism* / Q000473:pathology*; D003110:Colonic Neoplasms / Q000235:genetics*; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D035683:MicroRNAs / Q000235:genetics* / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods* / Q000592:standards; D012015:Reference Standards; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D035683:MicroRNAs