Network-based analysis of reverse phase protein array data

Rency S. Varghese; Yiming Zuo; Yi Zhao; Yong Wei Zhang; Sandra A. Jablonski; Mariaelena Pierobon; Emanuel F. Petricoin; Habtom W. Ressom; Louis M. Weiner

doi:10.1109/BIBM.2016.7822538

Network-based analysis of reverse phase protein array data

Rency S. Varghese, Yiming Zuo, Yi Zhao, Yong Wei Zhang, Sandra A. Jablonski, Mariaelena Pierobon, Emanuel F. Petricoin, Habtom W. Ressom, Louis M. Weiner^*

^*Corresponding author for this work

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

Abstract

In this paper, we introduce a computational method for constructing networks based on reverse phase protein array (RPPA) data to identify complex patterns in protein signaling. The method is applied to phosphoproteomic profiles of basal expression and activation/phosphorylation of 76 key signaling proteins in three breast cancer cell lines (MCF7, LCC1, and LCC9). Temporal RPPA data are acquired at 48h, 96h, and 144h after knocking down four genes in separate experiments. These genes are selected from a previous study as important determinants for breast cancer survival. Interaction networks between the proteins and phosphorylated proteins are constructed by analyzing the expression levels of protein pairs using a multivariate analysis of variance model. A new scoring criterion is introduced to determine the proteins that changed significantly at each of the three time points. Signaling networks are constructed based on statistically significant protein pairs selected from the RPPA data. Through a topology based analysis, we search for wiring patterns to help identify key network nodes that are associated with protein expression changes in various experimental conditions.

Original language	English
Title of host publication	Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
Editors	Kevin Burrage, Qian Zhu, Yunlong Liu, Tianhai Tian, Yadong Wang, Xiaohua Tony Hu, Qinghua Jiang, Jiangning Song, Shinichi Morishita, Kevin Burrage, Guohua Wang
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	312-317
Number of pages	6
ISBN (Electronic)	9781509016105
DOIs	https://doi.org/10.1109/BIBM.2016.7822538
State	Published - 17 Jan 2017
Externally published	Yes
Event	2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 - Shenzhen, China Duration: 15 Dec 2016 → 18 Dec 2016

Publication series

Name	Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016

Conference

Conference	2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016
Country/Territory	China
City	Shenzhen
Period	15/12/16 → 18/12/16

Keywords

Breast cancer
MANOVA
Network construction
RPPA
Topology analysis

Access to Document

10.1109/BIBM.2016.7822538

Cite this

Varghese, R. S., Zuo, Y., Zhao, Y., Zhang, Y. W., Jablonski, S. A., Pierobon, M., Petricoin, E. F., Ressom, H. W., & Weiner, L. M. (2017). Network-based analysis of reverse phase protein array data. In K. Burrage, Q. Zhu, Y. Liu, T. Tian, Y. Wang, X. T. Hu, Q. Jiang, J. Song, S. Morishita, K. Burrage, & G. Wang (Eds.), Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 (pp. 312-317). Article 7822538 (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2016.7822538

Varghese, Rency S. ; Zuo, Yiming ; Zhao, Yi et al. / Network-based analysis of reverse phase protein array data. Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. editor / Kevin Burrage ; Qian Zhu ; Yunlong Liu ; Tianhai Tian ; Yadong Wang ; Xiaohua Tony Hu ; Qinghua Jiang ; Jiangning Song ; Shinichi Morishita ; Kevin Burrage ; Guohua Wang. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 312-317 (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016).

@inproceedings{86c421ddb4f443298965c9700b7ab4d2,

title = "Network-based analysis of reverse phase protein array data",

abstract = "In this paper, we introduce a computational method for constructing networks based on reverse phase protein array (RPPA) data to identify complex patterns in protein signaling. The method is applied to phosphoproteomic profiles of basal expression and activation/phosphorylation of 76 key signaling proteins in three breast cancer cell lines (MCF7, LCC1, and LCC9). Temporal RPPA data are acquired at 48h, 96h, and 144h after knocking down four genes in separate experiments. These genes are selected from a previous study as important determinants for breast cancer survival. Interaction networks between the proteins and phosphorylated proteins are constructed by analyzing the expression levels of protein pairs using a multivariate analysis of variance model. A new scoring criterion is introduced to determine the proteins that changed significantly at each of the three time points. Signaling networks are constructed based on statistically significant protein pairs selected from the RPPA data. Through a topology based analysis, we search for wiring patterns to help identify key network nodes that are associated with protein expression changes in various experimental conditions.",

keywords = "Breast cancer, MANOVA, Network construction, RPPA, Topology analysis",

author = "Varghese, {Rency S.} and Yiming Zuo and Yi Zhao and Zhang, {Yong Wei} and Jablonski, {Sandra A.} and Mariaelena Pierobon and Petricoin, {Emanuel F.} and Ressom, {Habtom W.} and Weiner, {Louis M.}",

note = "Publisher Copyright: {\textcopyright} 2016 IEEE.; 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016 ; Conference date: 15-12-2016 Through 18-12-2016",

year = "2017",

month = jan,

day = "17",

doi = "10.1109/BIBM.2016.7822538",

language = "English",

series = "Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016",

publisher = "Institute of Electrical and Electronics Engineers Inc.",

pages = "312--317",

editor = "Kevin Burrage and Qian Zhu and Yunlong Liu and Tianhai Tian and Yadong Wang and Hu, {Xiaohua Tony} and Qinghua Jiang and Jiangning Song and Shinichi Morishita and Kevin Burrage and Guohua Wang",

booktitle = "Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016",

}

Varghese, RS, Zuo, Y, Zhao, Y, Zhang, YW, Jablonski, SA, Pierobon, M, Petricoin, EF, Ressom, HW & Weiner, LM 2017, Network-based analysis of reverse phase protein array data. in K Burrage, Q Zhu, Y Liu, T Tian, Y Wang, XT Hu, Q Jiang, J Song, S Morishita, K Burrage & G Wang (eds), Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016., 7822538, Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, Institute of Electrical and Electronics Engineers Inc., pp. 312-317, 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016, Shenzhen, China, 15/12/16. https://doi.org/10.1109/BIBM.2016.7822538

Network-based analysis of reverse phase protein array data. / Varghese, Rency S.; Zuo, Yiming; Zhao, Yi et al.
Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. ed. / Kevin Burrage; Qian Zhu; Yunlong Liu; Tianhai Tian; Yadong Wang; Xiaohua Tony Hu; Qinghua Jiang; Jiangning Song; Shinichi Morishita; Kevin Burrage; Guohua Wang. Institute of Electrical and Electronics Engineers Inc., 2017. p. 312-317 7822538 (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016).

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

TY - GEN

T1 - Network-based analysis of reverse phase protein array data

AU - Varghese, Rency S.

AU - Zuo, Yiming

AU - Zhao, Yi

AU - Zhang, Yong Wei

AU - Jablonski, Sandra A.

AU - Pierobon, Mariaelena

AU - Petricoin, Emanuel F.

AU - Ressom, Habtom W.

AU - Weiner, Louis M.

PY - 2017/1/17

Y1 - 2017/1/17

N2 - In this paper, we introduce a computational method for constructing networks based on reverse phase protein array (RPPA) data to identify complex patterns in protein signaling. The method is applied to phosphoproteomic profiles of basal expression and activation/phosphorylation of 76 key signaling proteins in three breast cancer cell lines (MCF7, LCC1, and LCC9). Temporal RPPA data are acquired at 48h, 96h, and 144h after knocking down four genes in separate experiments. These genes are selected from a previous study as important determinants for breast cancer survival. Interaction networks between the proteins and phosphorylated proteins are constructed by analyzing the expression levels of protein pairs using a multivariate analysis of variance model. A new scoring criterion is introduced to determine the proteins that changed significantly at each of the three time points. Signaling networks are constructed based on statistically significant protein pairs selected from the RPPA data. Through a topology based analysis, we search for wiring patterns to help identify key network nodes that are associated with protein expression changes in various experimental conditions.

AB - In this paper, we introduce a computational method for constructing networks based on reverse phase protein array (RPPA) data to identify complex patterns in protein signaling. The method is applied to phosphoproteomic profiles of basal expression and activation/phosphorylation of 76 key signaling proteins in three breast cancer cell lines (MCF7, LCC1, and LCC9). Temporal RPPA data are acquired at 48h, 96h, and 144h after knocking down four genes in separate experiments. These genes are selected from a previous study as important determinants for breast cancer survival. Interaction networks between the proteins and phosphorylated proteins are constructed by analyzing the expression levels of protein pairs using a multivariate analysis of variance model. A new scoring criterion is introduced to determine the proteins that changed significantly at each of the three time points. Signaling networks are constructed based on statistically significant protein pairs selected from the RPPA data. Through a topology based analysis, we search for wiring patterns to help identify key network nodes that are associated with protein expression changes in various experimental conditions.

KW - Breast cancer

KW - MANOVA

KW - Network construction

KW - RPPA

KW - Topology analysis

UR - http://www.scopus.com/inward/record.url?scp=85013249581&partnerID=8YFLogxK

U2 - 10.1109/BIBM.2016.7822538

DO - 10.1109/BIBM.2016.7822538

M3 - Conference contribution

AN - SCOPUS:85013249581

T3 - Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016

SP - 312

EP - 317

BT - Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016

A2 - Burrage, Kevin

A2 - Zhu, Qian

A2 - Liu, Yunlong

A2 - Tian, Tianhai

A2 - Wang, Yadong

A2 - Hu, Xiaohua Tony

A2 - Jiang, Qinghua

A2 - Song, Jiangning

A2 - Morishita, Shinichi

A2 - Burrage, Kevin

A2 - Wang, Guohua

PB - Institute of Electrical and Electronics Engineers Inc.

T2 - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016

Y2 - 15 December 2016 through 18 December 2016

ER -

Varghese RS, Zuo Y, Zhao Y, Zhang YW, Jablonski SA, Pierobon M et al. Network-based analysis of reverse phase protein array data. In Burrage K, Zhu Q, Liu Y, Tian T, Wang Y, Hu XT, Jiang Q, Song J, Morishita S, Burrage K, Wang G, editors, Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016. Institute of Electrical and Electronics Engineers Inc. 2017. p. 312-317. 7822538. (Proceedings - 2016 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2016). doi: 10.1109/BIBM.2016.7822538

Network-based analysis of reverse phase protein array data

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