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 co

SUBMITTER: Lee I 

PROVIDER: S-EPMC2275156 | biostudies-literature | 2008 Mar

REPOSITORIES: biostudies-literature