Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG).
Discriminating single-base difference miRNA expressions using microarray Probe Design Guru (ProDeG).
复制标题
使用微阵列探针设计大师（PODEG）区分单基差miRNA表达式。
DOI：
10.1093/nar/gkm1165
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发表时间：
2008-03
影响因子：
14.9
通讯作者：
Athey, Brian D.
中科院分区：
文献类型：
--
作者：
Lee, Inhan;Ajay, Subramanian S.;Chen, Haiming;Maruyama, Atsushi;Wang, Nulang;McInnis, Melvin G.;Athey, Brian D.
microRNA（miRNA）是一种内源性的组织特异性短RNA，可调控基因的表达。由于let-7的丰富性以及与发育和癌症的联系，区分每个let-7家族成员的表达尤其重要。然而，短的长度（22个核苷酸）和多个序列之间的相似性，阻止了个别成员的识别。在这里，我们提出了ProDeG，一种计算算法，设计不完全匹配的序列（以前在微阵列实验中只产生噪声水平）的全基因组微阵列“信号”探针，以区分单核苷酸差异，提高探针质量。我们的整个let-7家族的探针都是同质的和具体的，验证使用微阵列信号从荧光染料标记的寡核苷酸对应的let-7家族，证明了我们的算法的力量。此外，通过与我们的探针组信号进行比较，在淋巴母细胞样细胞系样品中鉴定了来自常规完全匹配探针的假let-7 c信号，引起了对常规微阵列平台中假let-7家族信号的关注。
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.
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