title: InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology.
abstract: The Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs. Without a graphical visualization interface, it is difficult for result interpretation.
  
  
  
  We present InteGO2, a web tool that allows researchers to calculate the GO-based gene semantic similarities using seven widely used GO-based similarity measurements. Also, we provide an integrative measurement that synergistically integrates all the individual measurements to improve the overall performance. Using HTML5 and cytoscape.js, we provide a graphical interface in InteGO2 to visualize the resulting gene functional association networks.
  
  
  
  InteGO2 is an easy-to-use HTML5 based web tool. With it, researchers can measure gene or gene product functional similarity conveniently, and visualize the network of functional interactions in a graphical interface. InteGO2 can be accessed via http://mlg.hit.edu.cn:8089/ .
authors: School of Computer Science, Northwestern Polytechnical University, Xi'an, China.|Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, 48824, MI, USA.
authors: Jiajie
authors: J
authors: Peng
authors: School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.
authors: Hongxiang
authors: H
authors: Li
authors: School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China.
authors: Yongzhuang
authors: Y
authors: Liu
authors: School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.
authors: Liran
authors: L
authors: Juan
authors: School of Life Science and Technology, Harbin Institute of Technology, Harbin, China.
authors: Qinghua
authors: Q
authors: Jiang
authors: School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China. ydwang@hit.edu.cn.
authors: Yadong
authors: Y
authors: Wang
authors: Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, 48824, MI, USA. jinchen@msu.edu.|Department of Computer Science and Engineering, Michigan State University, East Lansing, 48824, MI, USA. jinchen@msu.edu.
authors: Jin
authors: J
authors: Chen
mesh_terms: D000465:Algorithms; D019295:Computational Biology; D063990:Gene Ontology; D053263:Gene Regulatory Networks; D005798:Genes, Bacterial; D012984:Software
keywords: Gene Ontology; Semantic similarity; Web tool