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

Abstract

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.

Authors:
 [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:
Research Org.:
Michigan State Univ., East Lansing, MI (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1362018
Grant/Contract Number:  
FG02-91ER20021
Resource Type:
Accepted Manuscript
Journal Name:
BMC Genomics
Additional Journal Information:
Journal Volume: 17; Journal Issue: S5; Journal ID: ISSN 1471-2164
Publisher:
Springer
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; gene ontology; semantic similarity; web tool

Citation Formats

Peng, Jiajie, Li, Hongxiang, Liu, Yongzhuang, Juan, Liran, Jiang, Qinghua, Wang, Yadong, and Chen, Jin. InteGO2: A web tool for measuring and visualizing gene semantic similarities using Gene Ontology. United States: N. p., 2016. Web. doi:10.1186/s12864-016-2828-6.
Peng, Jiajie, Li, Hongxiang, Liu, Yongzhuang, Juan, Liran, Jiang, Qinghua, Wang, Yadong, & Chen, Jin. InteGO2: A web tool for measuring and visualizing gene semantic similarities using Gene Ontology. United States. doi:10.1186/s12864-016-2828-6.
Peng, Jiajie, Li, Hongxiang, Liu, Yongzhuang, Juan, Liran, Jiang, Qinghua, Wang, Yadong, and Chen, Jin. Wed . "InteGO2: A web tool for measuring and visualizing gene semantic similarities using Gene Ontology". United States. doi:10.1186/s12864-016-2828-6. https://www.osti.gov/servlets/purl/1362018.
@article{osti_1362018,
title = {InteGO2: A web tool for measuring and visualizing gene semantic similarities using Gene Ontology},
author = {Peng, Jiajie and Li, Hongxiang and Liu, Yongzhuang and Juan, Liran and Jiang, Qinghua and Wang, Yadong and Chen, Jin},
abstractNote = {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.},
doi = {10.1186/s12864-016-2828-6},
journal = {BMC Genomics},
number = S5,
volume = 17,
place = {United States},
year = {2016},
month = {8}
}

Journal Article:
Free Publicly Available Full Text
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Citation Metrics:
Cited by: 17 works
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Figures / Tables:

Fig. 1 Fig. 1: The user input interface of InteGO2. The inputs are grouped into three categories: a the input genes and related information, b choosing similarity measurement and GO category, and c user information

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Works referenced in this record:

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    journal, September 2017


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