Identification of Simple Sequence Repeat Biomarkers through Cross-Species Comparison in a Tag Cloud Representation

被引:4
作者
Huang, Jhen-Li [1 ]
Chang, Hao-Teng [2 ,3 ]
Cheng, Ronshan [4 ]
Hsu, Hui-Huang [5 ]
Pai, Tun-Wen [1 ]
机构
[1] Natl Taiwan Ocean Univ, Dept Comp Sci & Engn, Keelung 20224, Taiwan
[2] China Med Univ, Grad Inst Basic Med Sci, Taichung 40402, Taiwan
[3] Asia Univ, Dept Comp Sci & Informat Engn, Taichung 41354, Taiwan
[4] Natl Taiwan Ocean Univ, Dept Aquaculture, Keelung 20224, Taiwan
[5] Tamkang Univ, Dept Comp Sci & Informat Engn, New Taipei City 25137, Taiwan
关键词
MANDIBULOFACIAL DYSOSTOSIS; GENE ONTOLOGY; MICROSATELLITES;
D O I
10.1155/2014/678971
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
Simple sequence repeats (SSRs) are not only applied as genetic markers in evolutionary studies but they also play an important role in gene regulatory activities. Efficient identification of conserved and exclusive SSRs through cross-species comparison is helpful for understanding the evolutionary mechanisms and associations between specific gene groups and SSR motifs. In this paper, we developed an online cross-species comparative system and integrated it with a tag cloud visualization technique for identifying potential SSR biomarkers within fourteen frequently used model species. Ultraconserved or exclusive SSRs among cross-species orthologous genes could be effectively retrieved and displayed through a friendly interface design. Four different types of testing cases were applied to demonstrate and verify the retrieved SSR biomarker candidates. Through statistical analysis and enhanced tag cloud representation on defined functional related genes and cross-species clusters, the proposed system can correctly represent the patterns, loci, colors, and sizes of identified SSRs in accordance with gene functions, pattern qualities, and conserved characteristics among species.
引用
收藏
页数:11
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