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

Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang; Juan, Liran; Jiang, Qinghua; Wang, Yadong; Chen, Jin

doi:10.1186/s12864-016-2828-6

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

Journal Article · Wed Aug 31 00:00:00 EDT 2016 · BMC Genomics

DOI:https://doi.org/10.1186/s12864-016-2828-6· OSTI ID:1362018

Peng, Jiajie ^[1]; Li, Hongxiang ^[2]; Liu, Yongzhuang ^[2]; Juan, Liran ^[2]; Jiang, Qinghua ^[2]; Wang, Yadong ^[2]; Chen, Jin ^[3]

Northwestern Polytechnical Univ., Xi'an (China); Michigan State Univ., East Lansing, MI (United States)
Harbin Institute of Technology, Harbin (China)
Michigan State Univ., East Lansing, MI (United States)

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.

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Research Organization:: Michigan State Univ., East Lansing, MI (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: FG02-91ER20021

OSTI ID:: 1362018

Journal Information:: BMC Genomics, Vol. 17, Issue S5; ISSN 1471-2164

Publisher:: SpringerCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 24 works

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OAHG: an integrated resource for annotating human genes with multi-level ontologies Cheng, Liang; Sun, Jie; Xu, Wanying Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep34820	journal	October 2016
Identifying emerging phenomenon in long temporal phenotyping experiments Peng, Jiajie; Lu, Junya; Hoh, Donghee Bioinformatics https://doi.org/10.1093/bioinformatics/btz559	journal	July 2019
Refine gene functional similarity network based on interaction networks Tian, Zhen; Guo, Maozu; Wang, Chunyu BMC Bioinformatics, Vol. 18, Issue S16 https://doi.org/10.1186/s12859-017-1969-1	journal	December 2017
Predicting disease-related genes using integrated biomedical networks Peng, Jiajie; Bai, Kun; Shang, Xuequn BMC Genomics, Vol. 18, Issue S1 https://doi.org/10.1186/s12864-016-3263-4	journal	January 2017
An online tool for measuring and visualizing phenotype similarities using HPO Peng, Jiajie; Xue, Hansheng; Hui, Weiwei BMC Genomics, Vol. 19, Issue S6 https://doi.org/10.1186/s12864-018-4927-z	journal	August 2018
Constructing an integrated gene similarity network for the identification of disease genes Tian, Zhen; Guo, Maozu; Wang, Chunyu Journal of Biomedical Semantics, Vol. 8, Issue S1 https://doi.org/10.1186/s13326-017-0141-1	journal	September 2017
Constructing an integrated gene similarity network for the identification of disease genes 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) https://doi.org/10.1109/bibm.2016.7822768	conference	December 2016
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Investigations on factors influencing HPO-based semantic similarity calculation Peng, Jiajie; Li, Qianqian; Shang, Xuequn Journal of Biomedical Semantics, Vol. 8, Issue S1 https://doi.org/10.1186/s13326-017-0144-y	journal	September 2017

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InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology [Supplementary Data] Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang https://doi.org/10.6084/m9.figshare.c.3601337 The current record is supplemented by this collection	collection	August 2016
InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology [Supplementary Data] Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang https://doi.org/10.6084/m9.figshare.c.3601337.v1 The current record is supplemented by this dataset	dataset	August 2016
Additional file 1 of InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang https://doi.org/10.6084/m9.figshare.c.3601337_d1 The current record is supplemented by this text	text	January 2016
Additional file 1 of InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology Peng, Jiajie; Li, Hongxiang; Liu, Yongzhuang https://doi.org/10.6084/m9.figshare.c.3601337_d1.v1 The current record is supplemented by this preprint	preprint	August 2016