Paper Info
Title
Multiscale SSR Tag Cloud Visualization for Biomarker Discovery
Abstract
Tag cloud is an efficient visualization technique to help users rapidly understand the significant components within a tag based dataset. To make practical use of the visualization method, we proposed a cross-comparison mechanism for discovering Simple Sequence Repeat (SSR) biomarkers by annotating retrieved tag entries in various colors and font sizes to differentiate conservative status of two species groups. The identified SSR tag entries can represent the conservative and exclusive features among various species with respect to a specified functional gene set. Grouped SSR features of the same kind species can be classified and displayed simultaneously in order to compare evolutionary relationships. In addition, we applied different parameter settings for SSR discovery algorithms to generate multiscale tag clouds which provide different levels of significance of discovered repeat segments. In this study, several significant SSR patterns within eight skeletal development genes from 10 different species were illustrated and classified as notable features for the previously defined two groups of mammalian and fishery species. The proposed multiscale SSR tag clouds were demonstrated to be able to facilitate biologists on searching notable SSR biomarkers or putative gene regulatory elements in this study.
Year
DOI
Venue
2011
10.1109/CISIS.2011.85
CISIS
Keywords
Field
DocType
aquaculture,tag cloud,visualization,bioinformatics,tag clouds,data visualisation,genomics,cloud computing
Data mining,Data visualization,Computer science,Visualization,Genomics,Tag cloud,Biomarker discovery,Computational biology,Putative gene,Distributed computing
Conference
Citations 
PageRank 
References 
2
0.38
4
Authors
5
Name
Order
Citations
PageRank
Jhen-Li Huang121.39
Chien-Ming Chen2175.55
Tun-Wen Pai312729.71
Liang Wei Zeng420.38
Ron-Shan Cheng531.06