title: Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG).
abstract: MicroRNAs (miRNA) are endogenous tissue-specific short RNAs that regulate gene expression. Discriminating each let-7 family member expression is especially important due to let-7's abundance and connection with development and cancer. However, short lengths (22 nt) and similarities between multiple sequences have prevented identification of individual members. Here, we present ProDeG, a computational algorithm which designs imperfectly matched sequences (previously yielding only noise levels in microarray experiments) for genome-wide microarray "signal" probes to discriminate single nucleotide differences and to improve probe qualities. Our probes for the entire let-7 family are both homogeneous and specific, verified using microarray signals from fluorescent dye-tagged oligonucleotides corresponding to the let-7 family, demonstrating the power of our algorithm. In addition, false let-7c signals from conventional perfectly-matched probes were identified in lymphoblastoid cell-line samples through comparison with our probe-set signals, raising concerns about false let-7 family signals in conventional microarray platform.
authors.affiliation: Department of Psychiatry, University of Michigan, Ann Arbor, Bioinformatics Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA. inhan@umich.edu
authors.forename: Inhan
authors.initials: I
authors.lastname: Lee
authors.forename: Subramanian S
authors.initials: SS
authors.lastname: Ajay
authors.forename: Haiming
authors.initials: H
authors.lastname: Chen
authors.forename: Atsushi
authors.initials: A
authors.lastname: Maruyama
authors.forename: Nulang
authors.initials: N
authors.lastname: Wang
authors.forename: Melvin G
authors.initials: MG
authors.lastname: McInnis
authors.forename: Brian D
authors.initials: BD
authors.lastname: Athey
mesh_terms: D000465:Algorithms; D020137:Base Pair Mismatch; D002460:Cell Line; D018076:DNA, Complementary / Q000032:analysis; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000032:analysis / Q000737:chemistry / Q000378:metabolism*; D009691:Nucleic Acid Denaturation; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000737:chemistry*; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D018076:DNA, Complementary; D035683:MicroRNAs; D015345:Oligonucleotide Probes; C487931:mirnlet7 microRNA, human