GEsture: an online hand-drawing tool for gene expression pattern search

PeerJ

article

Chunyan Wang¹  Yiqing Xu¹  Xuelin Wang¹  Li Zhang¹  Suyun Wei¹  Qiaolin Ye¹  Youxiang Zhu¹  Hengfu Yin²  Manoj Nainwal³  Luis Tanon-Reyes⁴  Feng Cheng⁵  Tongming Yin⁶  Ning Ye¹ 

[1] College of Information Science and Technology, Nanjing Forestry University;Key Laboratory of Forest genetics and breeding, Research Institute of Subtropical Forestry;Department of Computer Science, Nantong University;Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida;Department of Pharmaceutical Science, College of Pharmacy, University of South Florida;College of Forest Resources and Environment, Nanjing Forestry University

关键词: Bioinformatics;    Gene expression;    Time series;    Hand-drawing;    Microarrays;   

DOI  :  10.7717/peerj.4927

学科分类：社会科学、人文和艺术（综合）

来源: Inra

【 摘 要 】

Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a ‘desirable’ or ‘user-defined’ pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with a gene expression curve as input from time series datasets. We presented three examples that illustrate the capacity of GEsture in gene hunting while following users’ requirements. GEsture also provides visualization tools (such as expression pattern figure, heat map and correlation network) to display the searching results. The result outputs may provide useful information for researchers to understand the targets, function and biological processes of the involved genes.

【 授权许可】

CC BY