Network based models and path based features for gene prioritization

Yuechang Liu; Hanghang Tong; Xie Lei; Yong Tang

doi:10.1109/CSCWD.2016.7565976

Network based models and path based features for gene prioritization

Yuechang Liu, Hanghang Tong, Xie Lei, Yong Tang

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

Network analysis has been shown to be an effective and cheap way to screen genes that are associated to diseases and chemicals. The identification of features that are used to order potentially related genes is key to do this job. Though many network models and structure based features have been proposed in the literature, they do not perform well enough for such gene prioritization task, especially when the heterogeneity of such networks is taken account. In this paper, a type of heterogenous network called Generalized Bi-relational Network (GBN) is formalized. A series of path based features on GBN are defined. Though some of the features have been used in other literature, it is the first time to evaluate them in both supervised and unsupervised learning models. The experiment on real chemical-disease-gene networks shows that the features proposed in this paper gain promising performance in both supervised and unsupervised framework.

Original language	English (US)
Title of host publication	Proceedings of the 2016 IEEE 20th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016
Editors	Xiaoping P. Liu, Jianming Yong, Jean-Paul Barthes, Weiming Shen, Chunsheng Yang, Junzhou Luo, Limin Chen
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	129-132
Number of pages	4
ISBN (Electronic)	9781509019151
DOIs	https://doi.org/10.1109/CSCWD.2016.7565976
State	Published - Sep 13 2016
Externally published	Yes
Event	20th IEEE International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016 - Nanchang, China Duration: May 4 2016 → May 6 2016

Publication series

Name	Proceedings of the 2016 IEEE 20th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016

Conference

Conference	20th IEEE International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016
Country/Territory	China
City	Nanchang
Period	5/4/16 → 5/6/16

Keywords

Generalized Bi-relation Network(GBN)
feature
gene prioritization
network analysis
path

ASJC Scopus subject areas

Management Information Systems
Artificial Intelligence
Computer Graphics and Computer-Aided Design
Computer Networks and Communications
Computer Science Applications

Online availability

10.1109/CSCWD.2016.7565976

Library availability

Discover UIUC Full Text

Cite this

Liu, Y., Tong, H., Lei, X., & Tang, Y. (2016). Network based models and path based features for gene prioritization. In X. P. Liu, J. Yong, J.-P. Barthes, W. Shen, C. Yang, J. Luo, & L. Chen (Eds.), Proceedings of the 2016 IEEE 20th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016 (pp. 129-132). Article 7565976 (Proceedings of the 2016 IEEE 20th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/CSCWD.2016.7565976

Network based models and path based features for gene prioritization. / Liu, Yuechang; Tong, Hanghang; Lei, Xie et al.
Proceedings of the 2016 IEEE 20th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016. ed. / Xiaoping P. Liu; Jianming Yong; Jean-Paul Barthes; Weiming Shen; Chunsheng Yang; Junzhou Luo; Limin Chen. Institute of Electrical and Electronics Engineers Inc., 2016. p. 129-132 7565976 (Proceedings of the 2016 IEEE 20th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Liu, Y, Tong, H, Lei, X & Tang, Y 2016, Network based models and path based features for gene prioritization. in XP Liu, J Yong, J-P Barthes, W Shen, C Yang, J Luo & L Chen (eds), Proceedings of the 2016 IEEE 20th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016., 7565976, Proceedings of the 2016 IEEE 20th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016, Institute of Electrical and Electronics Engineers Inc., pp. 129-132, 20th IEEE International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016, Nanchang, China, 5/4/16. https://doi.org/10.1109/CSCWD.2016.7565976

Liu Y, Tong H, Lei X, Tang Y. Network based models and path based features for gene prioritization. In Liu XP, Yong J, Barthes JP, Shen W, Yang C, Luo J, Chen L, editors, Proceedings of the 2016 IEEE 20th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016. Institute of Electrical and Electronics Engineers Inc. 2016. p. 129-132. 7565976. (Proceedings of the 2016 IEEE 20th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016). doi: 10.1109/CSCWD.2016.7565976

Liu, Yuechang ; Tong, Hanghang ; Lei, Xie et al. / Network based models and path based features for gene prioritization. Proceedings of the 2016 IEEE 20th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016. editor / Xiaoping P. Liu ; Jianming Yong ; Jean-Paul Barthes ; Weiming Shen ; Chunsheng Yang ; Junzhou Luo ; Limin Chen. Institute of Electrical and Electronics Engineers Inc., 2016. pp. 129-132 (Proceedings of the 2016 IEEE 20th International Conference on Computer Supported Cooperative Work in Design, CSCWD 2016).

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AB - Network analysis has been shown to be an effective and cheap way to screen genes that are associated to diseases and chemicals. The identification of features that are used to order potentially related genes is key to do this job. Though many network models and structure based features have been proposed in the literature, they do not perform well enough for such gene prioritization task, especially when the heterogeneity of such networks is taken account. In this paper, a type of heterogenous network called Generalized Bi-relational Network (GBN) is formalized. A series of path based features on GBN are defined. Though some of the features have been used in other literature, it is the first time to evaluate them in both supervised and unsupervised learning models. The experiment on real chemical-disease-gene networks shows that the features proposed in this paper gain promising performance in both supervised and unsupervised framework.

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Network based models and path based features for gene prioritization

Abstract

Publication series

Conference

Keywords

ASJC Scopus subject areas

Online availability

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