Characterisation of protein-protein interaction network base on ℓ1-norm optimisation

Benjamin Yee Shing Li; Lam Fat Yeung; Choujun Zhan; Genke Yang

doi:10.1109/BIBM.2013.6732547

Characterisation of protein-protein interaction network base on ℓ1-norm optimisation

Benjamin Yee Shing Li
, Lam Fat Yeung
, Choujun Zhan
, Genke Yang

Department of Electrical Engineering

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

4 Citations (Scopus)

Abstract

Knowledge of interactions between proteins is an importance piece of information on the understanding of cellular mechanism. One of the challenges is to quantify how similar the two protein-protein interaction (PPI) networks. To provide a candidate solution of this problem, a distance measure for PPI networks is proposed. This distance measure involves solving an optimisation problem with which the objective function being a weighted sum of topological and biological measure of an alignment respectively. To solve this problem, the projected subgradient method is employed.
To illustrate the performance and usage of this distance measure, it is applied to the PPI networks of herpesvirus family. Five herpesviruses: EpsteinBarr virus (EBV), Herpes simplex virus (HSV), Mouse Cytomegalovirus (mCMV), Kaposi's sarcoma-associated herpesvirus (KSHV) and Varicella zoster virus (VZV) are considered in this paper. PPI network distances of the five her-pesviruses are computed and visualized using multidimensional scaling (MDS). Results show that the distance measure can reflect the dissimilarity among organisms. In addition our algorithm can also separate herpesvirus subfamilies given only topological information of the PPI network.
© 2013 IEEE.

Original language	English
Title of host publication	Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine
Editors	Guo-Zheng Li, Xiaohua Hu
Publisher	IEEE
Pages	509-512
ISBN (Electronic)	978-1-4799-1309-1
ISBN (Print)	978-1-4799-1310-7
DOIs	https://doi.org/10.1109/BIBM.2013.6732547
Publication status	Published - Dec 2013
Event	2013 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2013) - Shanghai, China Duration: 18 Dec 2013 → 21 Dec 2013 https://ieeexplore.ieee.org/xpl/conhome/6716150/proceeding

Publication series

Name	IEEE International Conference on Bioinformatics and Biomedicine-BIBM
ISSN (Print)	2156-1125

Conference

Conference	2013 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2013)
Place	China
City	Shanghai
Period	18/12/13 → 21/12/13
Internet address	https://ieeexplore.ieee.org/xpl/conhome/6716150/proceeding

Funding

This work was support by City University of Hong Kong (Grant No. 7003016). The authors would like to thank Dr. Peter Uetz and Dr. Even Fossum who kindly provided their herpesvirus PPI dataset and explained in details.

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Research Keywords

MAREKS-DISEASE VIRUS
HERPESVIRUS
RESOURCE
GENOMES
YEAST
MAP

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10.1109/BIBM.2013.6732547

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Li, B. Y. S., Yeung, L. F., Zhan, C., & Yang, G. (2013). Characterisation of protein-protein interaction network base on ℓ1-norm optimisation. In G.-Z. Li, & X. Hu (Eds.), Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine (pp. 509-512). (IEEE International Conference on Bioinformatics and Biomedicine-BIBM). IEEE. https://doi.org/10.1109/BIBM.2013.6732547

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title = "Characterisation of protein-protein interaction network base on ℓ1-norm optimisation",

abstract = "Knowledge of interactions between proteins is an importance piece of information on the understanding of cellular mechanism. One of the challenges is to quantify how similar the two protein-protein interaction (PPI) networks. To provide a candidate solution of this problem, a distance measure for PPI networks is proposed. This distance measure involves solving an optimisation problem with which the objective function being a weighted sum of topological and biological measure of an alignment respectively. To solve this problem, the projected subgradient method is employed. To illustrate the performance and usage of this distance measure, it is applied to the PPI networks of herpesvirus family. Five herpesviruses: EpsteinBarr virus (EBV), Herpes simplex virus (HSV), Mouse Cytomegalovirus (mCMV), Kaposi's sarcoma-associated herpesvirus (KSHV) and Varicella zoster virus (VZV) are considered in this paper. PPI network distances of the five her-pesviruses are computed and visualized using multidimensional scaling (MDS). Results show that the distance measure can reflect the dissimilarity among organisms. In addition our algorithm can also separate herpesvirus subfamilies given only topological information of the PPI network. {\textcopyright} 2013 IEEE.",

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Li, BYS, Yeung, LF, Zhan, C & Yang, G 2013, Characterisation of protein-protein interaction network base on ℓ1-norm optimisation. in G-Z Li & X Hu (eds), Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine. IEEE International Conference on Bioinformatics and Biomedicine-BIBM, IEEE, pp. 509-512, 2013 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2013), Shanghai, China, 18/12/13. https://doi.org/10.1109/BIBM.2013.6732547

Characterisation of protein-protein interaction network base on ℓ1-norm optimisation. / Li, Benjamin Yee Shing; Yeung, Lam Fat; Zhan, Choujun et al.
Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine. ed. / Guo-Zheng Li; Xiaohua Hu. IEEE, 2013. p. 509-512 (IEEE International Conference on Bioinformatics and Biomedicine-BIBM).

Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

TY - GEN

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AU - Li, Benjamin Yee Shing

AU - Yeung, Lam Fat

AU - Zhan, Choujun

AU - Yang, Genke

PY - 2013/12

Y1 - 2013/12

N2 - Knowledge of interactions between proteins is an importance piece of information on the understanding of cellular mechanism. One of the challenges is to quantify how similar the two protein-protein interaction (PPI) networks. To provide a candidate solution of this problem, a distance measure for PPI networks is proposed. This distance measure involves solving an optimisation problem with which the objective function being a weighted sum of topological and biological measure of an alignment respectively. To solve this problem, the projected subgradient method is employed. To illustrate the performance and usage of this distance measure, it is applied to the PPI networks of herpesvirus family. Five herpesviruses: EpsteinBarr virus (EBV), Herpes simplex virus (HSV), Mouse Cytomegalovirus (mCMV), Kaposi's sarcoma-associated herpesvirus (KSHV) and Varicella zoster virus (VZV) are considered in this paper. PPI network distances of the five her-pesviruses are computed and visualized using multidimensional scaling (MDS). Results show that the distance measure can reflect the dissimilarity among organisms. In addition our algorithm can also separate herpesvirus subfamilies given only topological information of the PPI network. © 2013 IEEE.

AB - Knowledge of interactions between proteins is an importance piece of information on the understanding of cellular mechanism. One of the challenges is to quantify how similar the two protein-protein interaction (PPI) networks. To provide a candidate solution of this problem, a distance measure for PPI networks is proposed. This distance measure involves solving an optimisation problem with which the objective function being a weighted sum of topological and biological measure of an alignment respectively. To solve this problem, the projected subgradient method is employed. To illustrate the performance and usage of this distance measure, it is applied to the PPI networks of herpesvirus family. Five herpesviruses: EpsteinBarr virus (EBV), Herpes simplex virus (HSV), Mouse Cytomegalovirus (mCMV), Kaposi's sarcoma-associated herpesvirus (KSHV) and Varicella zoster virus (VZV) are considered in this paper. PPI network distances of the five her-pesviruses are computed and visualized using multidimensional scaling (MDS). Results show that the distance measure can reflect the dissimilarity among organisms. In addition our algorithm can also separate herpesvirus subfamilies given only topological information of the PPI network. © 2013 IEEE.

KW - MAREKS-DISEASE VIRUS

KW - HERPESVIRUS

KW - RESOURCE

KW - GENOMES

KW - YEAST

KW - MAP

UR - https://www.scopus.com/pages/publications/84894595107

UR - https://www.scopus.com/pages/publications/84894595107#tab=impact

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M3 - RGC 32 - Refereed conference paper (with host publication)

SN - 978-1-4799-1310-7

T3 - IEEE International Conference on Bioinformatics and Biomedicine-BIBM

SP - 509

EP - 512

BT - Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine

A2 - Li, Guo-Zheng

A2 - Hu, Xiaohua

PB - IEEE

T2 - 2013 IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM 2013)

Y2 - 18 December 2013 through 21 December 2013

ER -

Characterisation of protein-protein interaction network base on ℓ1-norm optimisation

Abstract

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Funding

UN SDGs

Research Keywords

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