Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG).
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.
Lee
Inhan
I
Department of Psychiatry, University of Michigan, Ann Arbor, Bioinformatics Graduate Program, University of Michigan, Ann Arbor, MI 48109, USA. inhan@umich.edu
Ajay
Subramanian S
SS
Chen
Haiming
H
Maruyama
Atsushi
A
Wang
Nulang
N
McInnis
Melvin G
MG
Athey
Brian D
BD
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
D018076:DNA, Complementary; D035683:MicroRNAs; D015345:Oligonucleotide Probes; C487931:mirnlet7 microRNA, human