Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG)

作者：Lee Inhan^*; Ajay Subramanian S; Chen Haiming; Maruyama Atsushi; Wang Nulang; McInnis Melvin G; Athey Brian D

来源：Nucleic Acids Research, 2008, 36(5): e27.

DOI：10.1093/nar/gkm1165

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 oligo-nucleotides 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.

• 出版日期2008-3