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Title: InteGO2: A web tool for measuring and visualizing gene semantic similarities using Gene Ontology

Here, 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. As a result, 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. In conclusion, 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.
 [1] ;  [2] ;  [2] ;  [2] ;  [2] ;  [2] ;  [3]
  1. Northwestern Polytechnical Univ., Xi'an (China); Michigan State Univ., East Lansing, MI (United States)
  2. Harbin Institute of Technology, Harbin (China)
  3. Michigan State Univ., East Lansing, MI (United States)
Publication Date:
Grant/Contract Number:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 17; Journal Issue: S5; Journal ID: ISSN 1471-2164
Research Org:
Michigan State Univ., East Lansing, MI (United States)
Sponsoring Org:
Country of Publication:
United States
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; gene ontology; semantic similarity; web tool
OSTI Identifier: