title: Retrieving relevant experiments: The case of microRNA microarrays.
abstract: Content-based retrieval of biological experiments in large public repositories is a recent challenge in computational biology and bioinformatics. The task is, in general, to search in a database using a query-by-example without any experimental meta-data annotation. Here, we consider a more specific problem that seeks a solution for retrieving relevant microRNA experiments from microarray repositories. A computational framework is proposed with this objective. The framework adapts a normal-uniform mixture model for identifying differentially expressed microRNAs in microarray profiling experiments. A rank-based thresholding scheme is offered to binarize real-valued experiment fingerprints based on differential expression. An effective similarity metric is introduced to compare categorical fingerprints, which in turn infers the relevance between two experiments. Two different views of experimental relevance are evaluated, one for disease association and another for embryonic germ layer, to discern the retrieval ability of the proposed model. To the best of our knowledge, the experiment retrieval task is investigated for the first time in the context of microRNA microarrays.
authors.affiliation: Department of Computer Engineering, Başkent University, Ankara, Turkey.
authors.forename: Koray
authors.initials: K
authors.lastname: Açıcı
authors.affiliation: Department of Medical Genetics, Başkent University, Ankara, Turkey.
authors.forename: Yunus Kasım
authors.initials: YK
authors.lastname: Terzi
authors.affiliation: Department of Computer Engineering, Başkent University, Ankara, Turkey. Electronic address: hogul@baskent.edu.tr.
authors.forename: Hasan
authors.initials: H
authors.lastname: Oğul
mesh_terms: D036262:Empirical Research; D035683:MicroRNAs / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis
chemical_list: D035683:MicroRNAs
keywords: Database search; Gene expression; Information retrieval; microRNA regulation