Nucleic Acids Research Advance Access published online on January 21, 2008
Nucleic Acids Research, doi:10.1093/nar/gkm1165
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Methods Online |
Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG)
1Department of Psychiatry, University of Michigan, Ann Arbor, 2Bioinformatics Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA, 3Institute of Materials Chemistry and Engineering, Kyushu University, Fukuoka 819-0395, Japan, 4National Center for Integrated Biomedical Informatics, Ann Arbor and 5Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI 48109, USA
*To whom correspondence should be addressed. Tel: +1 734 232 0339; Fax: +1 734 615 8739; Email: inhan{at}umich.edu
Received June 22, 2007. Revised November 21, 2007. Accepted December 18, 2007.
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.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.