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

TitleDiscriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG).
Publication TypeJournal Article
Year of Publication2008
AuthorsLee, Inhan, Ajay Subramanian S., Chen Haiming, Maruyama Atsushi, Wang Nulang, McInnis Melvin G., and Athey Brian D.
JournalNucleic Acids Res
Volume36
Issue5
Paginatione27
Date Published2008 Mar
ISSN1362-4962
KeywordsAlgorithms, Base Pair Mismatch, Cell Line, DNA, Complementary, Gene Expression Profiling, Humans, MicroRNAs, Nucleic Acid Denaturation, Oligonucleotide Array Sequence Analysis, Oligonucleotide Probes, Reverse Transcriptase Polymerase Chain Reaction
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.

DOI10.1093/nar/gkm1165
Alternate JournalNucleic Acids Res.
PubMed ID18208839
PubMed Central IDPMC2275156
Grant ListMH064596 / MH / NIMH NIH HHS / United States
U54-DA021519 / DA / NIDA NIH HHS / United States