Deciphering Chemically-Induced Reversible Neurotoxicity by Reconstructing Perturbed Pathways From Time Series Microarray Gene Expression Data

Yi Yang; Si Li; Andrew S. Maxwell; Natalie D. Barker; Yan Peng; Ying Li; Haoni Li; Xi Wu; Peng Li; Tao Huang; Chenhua Zheng; Nan Wang; Edward J. Perkins; Chaoyang Zhang; Ping Gong

Deciphering Chemically-Induced Reversible Neurotoxicity by Reconstructing Perturbed Pathways From Time Series Microarray Gene Expression Data

Yi Yang, Si Li, Andrew S. Maxwell, Natalie D. Barker, Yan Peng, Ying Li, Haoni Li, Xi Wu, Peng Li, Tao Huang, Chenhua Zheng, Nan Wang, Edward J. Perkins, Chaoyang Zhang, Ping Gong

Department of Art and Design

Research output: Contribution to journal › Article › peer-review

Abstract

The etiology of chemically-induced neurotoxicity like seizures is poorly understood. Using reversible neurotoxicity induced by two neurotoxicants as example, we demonstrate that a bioinformatics-guided reverse engineering approach can be applied to analyze time series microarray gene expression data and uncover the underlying molecular mechanism. Our results reinforce previous findings that cholinergic and GABAergic synapse pathways are the target of carbaryl and RDX, respectively. We also conclude that perturbations to these pathways by sublethal concentrations of RDX and carbaryl were temporary, and earthworms were capable of fully recovering at the end of the 7-day recovery phase. In addition, our study indicates that many pathways other than those related to synaptic and neuronal activities were altered during the 6-day exposure phase. © 2013 IEEE.

Original language	American English
Journal	Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics
State	Published - Dec 1 2013

Keywords

KEGG pathway
differential gene interaction network
earthworm
reversible neurotoxicity
time course gene expression dataset

Disciplines

Computer Sciences
Physical Sciences and Mathematics

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https://doi.org/10.1109/GENSIPS.2013.6735927

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Yang, Y., Li, S., Maxwell, A. S., Barker, N. D., Peng, Y., Li, Y., Li, H., Wu, X., Li, P., Huang, T., Zheng, C., Wang, N., Perkins, E. J., Zhang, C., & Gong, P. (2013). Deciphering Chemically-Induced Reversible Neurotoxicity by Reconstructing Perturbed Pathways From Time Series Microarray Gene Expression Data. Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics. https://doi.org/10.1109/GENSIPS.2013.6735927

Yang, Y, Li, S, Maxwell, AS, Barker, ND, Peng, Y, Li, Y, Li, H, Wu, X, Li, P, Huang, T, Zheng, C, Wang, N, Perkins, EJ, Zhang, C & Gong, P 2013, 'Deciphering Chemically-Induced Reversible Neurotoxicity by Reconstructing Perturbed Pathways From Time Series Microarray Gene Expression Data', Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics. <https://doi.org/10.1109/GENSIPS.2013.6735927>

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title = "Deciphering Chemically-Induced Reversible Neurotoxicity by Reconstructing Perturbed Pathways From Time Series Microarray Gene Expression Data",

abstract = " The etiology of chemically-induced neurotoxicity like seizures is poorly understood. Using reversible neurotoxicity induced by two neurotoxicants as example, we demonstrate that a bioinformatics-guided reverse engineering approach can be applied to analyze time series microarray gene expression data and uncover the underlying molecular mechanism. Our results reinforce previous findings that cholinergic and GABAergic synapse pathways are the target of carbaryl and RDX, respectively. We also conclude that perturbations to these pathways by sublethal concentrations of RDX and carbaryl were temporary, and earthworms were capable of fully recovering at the end of the 7-day recovery phase. In addition, our study indicates that many pathways other than those related to synaptic and neuronal activities were altered during the 6-day exposure phase. {\textcopyright} 2013 IEEE.",

keywords = "KEGG pathway, differential gene interaction network, earthworm, reversible neurotoxicity, time course gene expression dataset",

author = "Yi Yang and Si Li and Maxwell, \{Andrew S.\} and Barker, \{Natalie D.\} and Yan Peng and Ying Li and Haoni Li and Xi Wu and Peng Li and Tao Huang and Chenhua Zheng and Nan Wang and Perkins, \{Edward J.\} and Chaoyang Zhang and Ping Gong",

year = "2013",

month = dec,

day = "1",

language = "American English",

journal = "Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics",

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TY - JOUR

T1 - Deciphering Chemically-Induced Reversible Neurotoxicity by Reconstructing Perturbed Pathways From Time Series Microarray Gene Expression Data

AU - Yang, Yi

AU - Li, Si

AU - Maxwell, Andrew S.

AU - Barker, Natalie D.

AU - Peng, Yan

AU - Li, Ying

AU - Li, Haoni

AU - Wu, Xi

AU - Li, Peng

AU - Huang, Tao

AU - Zheng, Chenhua

AU - Wang, Nan

AU - Perkins, Edward J.

AU - Zhang, Chaoyang

AU - Gong, Ping

PY - 2013/12/1

Y1 - 2013/12/1

N2 - The etiology of chemically-induced neurotoxicity like seizures is poorly understood. Using reversible neurotoxicity induced by two neurotoxicants as example, we demonstrate that a bioinformatics-guided reverse engineering approach can be applied to analyze time series microarray gene expression data and uncover the underlying molecular mechanism. Our results reinforce previous findings that cholinergic and GABAergic synapse pathways are the target of carbaryl and RDX, respectively. We also conclude that perturbations to these pathways by sublethal concentrations of RDX and carbaryl were temporary, and earthworms were capable of fully recovering at the end of the 7-day recovery phase. In addition, our study indicates that many pathways other than those related to synaptic and neuronal activities were altered during the 6-day exposure phase. © 2013 IEEE.

AB - The etiology of chemically-induced neurotoxicity like seizures is poorly understood. Using reversible neurotoxicity induced by two neurotoxicants as example, we demonstrate that a bioinformatics-guided reverse engineering approach can be applied to analyze time series microarray gene expression data and uncover the underlying molecular mechanism. Our results reinforce previous findings that cholinergic and GABAergic synapse pathways are the target of carbaryl and RDX, respectively. We also conclude that perturbations to these pathways by sublethal concentrations of RDX and carbaryl were temporary, and earthworms were capable of fully recovering at the end of the 7-day recovery phase. In addition, our study indicates that many pathways other than those related to synaptic and neuronal activities were altered during the 6-day exposure phase. © 2013 IEEE.

KW - KEGG pathway

KW - differential gene interaction network

KW - earthworm

KW - reversible neurotoxicity

KW - time course gene expression dataset

UR - https://aquila.usm.edu/fac_pubs/17934

UR - https://doi.org/10.1109/GENSIPS.2013.6735927

M3 - Article

JO - Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics

JF - Proceedings - IEEE International Workshop on Genomic Signal Processing and Statistics

ER -

Deciphering Chemically-Induced Reversible Neurotoxicity by Reconstructing Perturbed Pathways From Time Series Microarray Gene Expression Data

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Keywords

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