A network-based approach to mine temporal genes exhibiting significant expression variation in Caenorhabditis elegans

Kathryn Cooper; Wail Hassan; Hesham Ali

doi:10.1109/BIBM.2017.8217991

A network-based approach to mine temporal genes exhibiting significant expression variation in Caenorhabditis elegans

Kathryn Cooper, Wail Hassan, Hesham Ali

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

Abstract

It is critical to be able to identify longitudinally changing genes in temporal data so that studies can be focused on how gene expression changes in a dynamic way. While biological networks continue to play a significant role in modeling and characterizing complex relationships in biological systems, most network modeling studies in biomedical research focus on snapshot or 'static' network-based analysis to identify genes of interest. In this study, we use a temporal non-sampling network-based approach to identify and rank genes that exhibit significant co-expression variation over time. We use in the C. elegans gene correlation network obtained from mRNA expression profiles to illustrate the value of the proposed approach. We compare the results of this method to results obtained from traditional statistical analysis that focuses on identifying simple differentially expressed genes. We show that rank-based temporal network analysis can identify genes that contribute to changes in the network structure and consequently contribute to changes in the genetic regulatory machine.

Original language	English (US)
Title of host publication	Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Editors	Illhoi Yoo, Jane Huiru Zheng, Yang Gong, Xiaohua Tony Hu, Chi-Ren Shyu, Yana Bromberg, Jean Gao, Dmitry Korkin
Publisher	Institute of Electrical and Electronics Engineers Inc.
Pages	2151-2156
Number of pages	6
ISBN (Electronic)	9781509030491
DOIs	https://doi.org/10.1109/BIBM.2017.8217991
State	Published - Dec 15 2017
Event	2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 - Kansas City, United States Duration: Nov 13 2017 → Nov 16 2017

Publication series

Name	Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Volume	2017-January

Other

Other	2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Country/Territory	United States
City	Kansas City
Period	11/13/17 → 11/16/17

Keywords

bioinformatics algorithms
co-expression networks
gene expression
temporal network analysis

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics

Access to Document

10.1109/BIBM.2017.8217991

Cite this

Cooper, K., Hassan, W., & Ali, H. (2017). A network-based approach to mine temporal genes exhibiting significant expression variation in Caenorhabditis elegans. In I. Yoo, J. H. Zheng, Y. Gong, X. T. Hu, C.-R. Shyu, Y. Bromberg, J. Gao, & D. Korkin (Eds.), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017 (pp. 2151-2156). (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January). Institute of Electrical and Electronics Engineers Inc.. https://doi.org/10.1109/BIBM.2017.8217991

A network-based approach to mine temporal genes exhibiting significant expression variation in Caenorhabditis elegans. / Cooper, Kathryn; Hassan, Wail; Ali, Hesham.
Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. ed. / Illhoi Yoo; Jane Huiru Zheng; Yang Gong; Xiaohua Tony Hu; Chi-Ren Shyu; Yana Bromberg; Jean Gao; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. p. 2151-2156 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; Vol. 2017-January).

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

Cooper, K, Hassan, W & Ali, H 2017, A network-based approach to mine temporal genes exhibiting significant expression variation in Caenorhabditis elegans. in I Yoo, JH Zheng, Y Gong, XT Hu, C-R Shyu, Y Bromberg, J Gao & D Korkin (eds), Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, vol. 2017-January, Institute of Electrical and Electronics Engineers Inc., pp. 2151-2156, 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017, Kansas City, United States, 11/13/17. https://doi.org/10.1109/BIBM.2017.8217991

Cooper K, Hassan W, Ali H. A network-based approach to mine temporal genes exhibiting significant expression variation in Caenorhabditis elegans. In Yoo I, Zheng JH, Gong Y, Hu XT, Shyu CR, Bromberg Y, Gao J, Korkin D, editors, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Institute of Electrical and Electronics Engineers Inc. 2017. p. 2151-2156. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017). doi: 10.1109/BIBM.2017.8217991

Cooper, Kathryn ; Hassan, Wail ; Ali, Hesham. / A network-based approach to mine temporal genes exhibiting significant expression variation in Caenorhabditis elegans. Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. editor / Illhoi Yoo ; Jane Huiru Zheng ; Yang Gong ; Xiaohua Tony Hu ; Chi-Ren Shyu ; Yana Bromberg ; Jean Gao ; Dmitry Korkin. Institute of Electrical and Electronics Engineers Inc., 2017. pp. 2151-2156 (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017).

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A network-based approach to mine temporal genes exhibiting significant expression variation in Caenorhabditis elegans

Abstract

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Keywords

ASJC Scopus subject areas

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