title: GESearch: An Interactive GUI Tool for Identifying Gene Expression Signature.
abstract: The huge amount of gene expression data generated by microarray and next-generation sequencing technologies present challenges to exploit their biological meanings. When searching for the coexpression genes, the data mining process is largely affected by selection of algorithms. Thus, it is highly desirable to provide multiple options of algorithms in the user-friendly analytical toolkit to explore the gene expression signatures. For this purpose, we developed GESearch, an interactive graphical user interface (GUI) toolkit, which is written in MATLAB and supports a variety of gene expression data files. This analytical toolkit provides four models, including the mean, the regression, the delegate, and the ensemble models, to identify the coexpression genes, and enables the users to filter data and to select gene expression patterns by browsing the display window or by importing knowledge-based genes. Subsequently, the utility of this analytical toolkit is demonstrated by analyzing two sets of real-life microarray datasets from cell-cycle experiments. Overall, we have developed an interactive GUI toolkit that allows for choosing multiple algorithms for analyzing the gene expression signatures.
authors.affiliation: The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing 210037, China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing 210037, China.
authors.forename: Ning
authors.initials: N
authors.lastname: Ye
authors.affiliation: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China ; Key Laboratory of Forest genetics and breeding, Chinese Academy of Forestry, Fuyang, Zhejiang 311400, China.
authors.forename: Hengfu
authors.initials: H
authors.lastname: Yin
authors.affiliation: The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing 210037, China ; College of Forest Resources and Environment, Nanjing Forestry University, Nanjing 210037, China.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Liu
authors.affiliation: The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing 210037, China ; College of Forest Resources and Environment, Nanjing Forestry University, Nanjing 210037, China.
authors.forename: Xiaogang
authors.initials: X
authors.lastname: Dai
authors.affiliation: The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing 210037, China ; College of Forest Resources and Environment, Nanjing Forestry University, Nanjing 210037, China.
authors.forename: Tongming
authors.initials: T
authors.lastname: Yin
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D057225:Data Mining; D030541:Databases, Genetic; D005786:Gene Expression Regulation / Q000235:genetics*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D012984:Software; D059467:Transcriptome