Detecting pathway cross-talks by analyzing conserved functional modules across multiple phenotype-expressing organisms

Kevin Wilson, Andrea M. Rocha, Kanchana Padmanabhan, Kuangyu Wang, Zhengzhang Chen, Ye Jin, James R. Mihelcic, Nagiza F. Samatova

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

Abstract

Biological systems are organized hierarchically, starting from the protein level and expanding to pathway or even higher levels. Understanding interactions at lower levels (proteins interactions) in the hierarchy will help us understand interactions at higher levels (pathway cross-talks). Identifying cross-talks that are related to the expression of a particular phenotype will be of interest to genetic engineers, because it will provide information on how different cellular subsystems could work together to express a phenotype. Current research has typically focused on identifying genotype-phenotype associations or pathway-phenotype associations. In contrast, we developed a method to identify phenotype-related pathway cross talks by obtaining conserved groups of interacting proteins (functional modules). By applying our method to two groups of hydrogen producing organisms (light fermentation and dark fermentation), we have shown that our method effectively unearths known pathway cross-talks that are important to hydrogen production.

Original languageEnglish
Title of host publicationProceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011
Pages443-449
Number of pages7
DOIs
Publication statusPublished - 1 Dec 2011
Event2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011 - Atlanta, GA, United States
Duration: 12 Nov 201115 Nov 2011

Other

Other2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011
CountryUnited States
CityAtlanta, GA
Period12/11/1115/11/11

Fingerprint

Proteins
Phenotype
Fermentation
Hydrogen
Biological systems
Hydrogen production
Genetic Association Studies
Engineers
Light
Research

Keywords

  • cross-talk
  • pathway
  • phenotype-expressing organism
  • protein functional module

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Cite this

Wilson, K., Rocha, A. M., Padmanabhan, K., Wang, K., Chen, Z., Jin, Y., ... Samatova, N. F. (2011). Detecting pathway cross-talks by analyzing conserved functional modules across multiple phenotype-expressing organisms. In Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011 (pp. 443-449). [6120483] https://doi.org/10.1109/BIBM.2011.35

Detecting pathway cross-talks by analyzing conserved functional modules across multiple phenotype-expressing organisms. / Wilson, Kevin; Rocha, Andrea M.; Padmanabhan, Kanchana; Wang, Kuangyu; Chen, Zhengzhang; Jin, Ye; Mihelcic, James R.; Samatova, Nagiza F.

Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011. 2011. p. 443-449 6120483.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Wilson, K, Rocha, AM, Padmanabhan, K, Wang, K, Chen, Z, Jin, Y, Mihelcic, JR & Samatova, NF 2011, Detecting pathway cross-talks by analyzing conserved functional modules across multiple phenotype-expressing organisms. in Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011., 6120483, pp. 443-449, 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011, Atlanta, GA, United States, 12/11/11. https://doi.org/10.1109/BIBM.2011.35
Wilson K, Rocha AM, Padmanabhan K, Wang K, Chen Z, Jin Y et al. Detecting pathway cross-talks by analyzing conserved functional modules across multiple phenotype-expressing organisms. In Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011. 2011. p. 443-449. 6120483 https://doi.org/10.1109/BIBM.2011.35
Wilson, Kevin ; Rocha, Andrea M. ; Padmanabhan, Kanchana ; Wang, Kuangyu ; Chen, Zhengzhang ; Jin, Ye ; Mihelcic, James R. ; Samatova, Nagiza F. / Detecting pathway cross-talks by analyzing conserved functional modules across multiple phenotype-expressing organisms. Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011. 2011. pp. 443-449
@inproceedings{3e0e244217c44cff8b33d8f62739864c,
title = "Detecting pathway cross-talks by analyzing conserved functional modules across multiple phenotype-expressing organisms",
abstract = "Biological systems are organized hierarchically, starting from the protein level and expanding to pathway or even higher levels. Understanding interactions at lower levels (proteins interactions) in the hierarchy will help us understand interactions at higher levels (pathway cross-talks). Identifying cross-talks that are related to the expression of a particular phenotype will be of interest to genetic engineers, because it will provide information on how different cellular subsystems could work together to express a phenotype. Current research has typically focused on identifying genotype-phenotype associations or pathway-phenotype associations. In contrast, we developed a method to identify phenotype-related pathway cross talks by obtaining conserved groups of interacting proteins (functional modules). By applying our method to two groups of hydrogen producing organisms (light fermentation and dark fermentation), we have shown that our method effectively unearths known pathway cross-talks that are important to hydrogen production.",
keywords = "cross-talk, pathway, phenotype-expressing organism, protein functional module",
author = "Kevin Wilson and Rocha, {Andrea M.} and Kanchana Padmanabhan and Kuangyu Wang and Zhengzhang Chen and Ye Jin and Mihelcic, {James R.} and Samatova, {Nagiza F.}",
year = "2011",
month = "12",
day = "1",
doi = "10.1109/BIBM.2011.35",
language = "English",
isbn = "9780769545745",
pages = "443--449",
booktitle = "Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011",

}

TY - GEN

T1 - Detecting pathway cross-talks by analyzing conserved functional modules across multiple phenotype-expressing organisms

AU - Wilson, Kevin

AU - Rocha, Andrea M.

AU - Padmanabhan, Kanchana

AU - Wang, Kuangyu

AU - Chen, Zhengzhang

AU - Jin, Ye

AU - Mihelcic, James R.

AU - Samatova, Nagiza F.

PY - 2011/12/1

Y1 - 2011/12/1

N2 - Biological systems are organized hierarchically, starting from the protein level and expanding to pathway or even higher levels. Understanding interactions at lower levels (proteins interactions) in the hierarchy will help us understand interactions at higher levels (pathway cross-talks). Identifying cross-talks that are related to the expression of a particular phenotype will be of interest to genetic engineers, because it will provide information on how different cellular subsystems could work together to express a phenotype. Current research has typically focused on identifying genotype-phenotype associations or pathway-phenotype associations. In contrast, we developed a method to identify phenotype-related pathway cross talks by obtaining conserved groups of interacting proteins (functional modules). By applying our method to two groups of hydrogen producing organisms (light fermentation and dark fermentation), we have shown that our method effectively unearths known pathway cross-talks that are important to hydrogen production.

AB - Biological systems are organized hierarchically, starting from the protein level and expanding to pathway or even higher levels. Understanding interactions at lower levels (proteins interactions) in the hierarchy will help us understand interactions at higher levels (pathway cross-talks). Identifying cross-talks that are related to the expression of a particular phenotype will be of interest to genetic engineers, because it will provide information on how different cellular subsystems could work together to express a phenotype. Current research has typically focused on identifying genotype-phenotype associations or pathway-phenotype associations. In contrast, we developed a method to identify phenotype-related pathway cross talks by obtaining conserved groups of interacting proteins (functional modules). By applying our method to two groups of hydrogen producing organisms (light fermentation and dark fermentation), we have shown that our method effectively unearths known pathway cross-talks that are important to hydrogen production.

KW - cross-talk

KW - pathway

KW - phenotype-expressing organism

KW - protein functional module

UR - http://www.scopus.com/inward/record.url?scp=84862950699&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84862950699&partnerID=8YFLogxK

U2 - 10.1109/BIBM.2011.35

DO - 10.1109/BIBM.2011.35

M3 - Conference contribution

SN - 9780769545745

SP - 443

EP - 449

BT - Proceedings - 2011 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2011

ER -