MetaMirClust: Discovery of miRNA cluster patterns using a data-mining approach

被引：39
作者：
Chan, Wen-Ching [1 ,2 ,3 ]
Ho, Meng-Ru [4 ]
Li, Sung-Chou [4 ]
Tsai, Kuo-Wang [6 ]
Lai, Chun-Hung [5 ]
Hsu, Chun-Nan [3 ,7 ]
Lin, Wen-Chang [1 ,5 ]
机构：
[1] Natl Yang Ming Univ, Acad Sinica, Inst Biomed Informat, Taipei 112, Taiwan
[2] Acad Sinica, Taiwan Int Grad Program, Bioinformat Program, Taipei 115, Taiwan
[3] Acad Sinica, Inst Informat Sci, Taipei 115, Taiwan
[4] Acad Sinica, Genom Res Ctr, Taipei 115, Taiwan
[5] Acad Sinica, Inst Biomed Sci, Taipei 115, Taiwan
[6] Kaohsiung Vet Gen Hosp, Dept Med Educ & Res, Kaohsiung, Taiwan
[7] Univ So Calif, Inst Informat Sci, Marina Del Rey, CA 90292 USA
来源：
GENOMICS | 2012年 / 100卷 / 03期
关键词：
MicroRNA; MiRNA cluster; Data mining; Metazoan; COMPUTATIONAL IDENTIFICATION; GENOMIC ORGANIZATION; FREQUENT PATTERNS; MICRORNA GENES; MOUSE; MATURATION; EVOLUTION; MIR-17-92;
D O I：
10.1016/j.ygeno.2012.06.007
中图分类号：
Q81 [生物工程学（生物技术）]; Q93 [微生物学];
学科分类号：
071005 ; 0836 ; 090102 ; 100705 ;
摘要：
Recent genome-wide surveys on ncRNA have revealed that a substantial fraction of miRNA genes is likely to form clusters. However, the evolutionary and biological function implications of clustered miRNAs are still elusive. After identifying clustered miRNA genes under different maximum inter-miRNA distances (MIDs), this study intended to reveal evolution conservation patterns among these clustered miRNA genes in metazoan species using a computation algorithm. As examples, a total of 15-35% of known and predicted miRNA genes in nine selected species constitute clusters under the MIDs ranging from 1 kb to 50 kb. Intriguingly, 33 out of 37 metazoan miRNA clusters in 56 metazoan genomes are co-conserved with their up/down-stream adjacent protein-coding genes. Meanwhile, a co-expression pattern of miR-1 and miR-133a in the mir-133-1 cluster has been experimentally demonstrated. Therefore, the MetaMirClust database provides a useful bioinformatic resource for biologists to facilitate the advanced interrogations on the composition of miRNA clusters and their evolution patterns. (C) 2012 Elsevier Inc. All rights reserved.
引用
收藏
页码：141 / 148
页数：8
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