Temporal dynamics of protein complexes in PPI Networks: a case study using yeast cell cycle dynamics

Srihari, Sriganesh and Leong, Hon Wai (2012). Temporal dynamics of protein complexes in PPI Networks: a case study using yeast cell cycle dynamics. In: Proceedings of Asia Pacific Bioinformatics Network (APBioNet) 11th International Conference on Bioinformatics (InCoB). Asia Pacific Bioinformatics Network (APBioNet) 11th International Conference on Bioinformatics (InCoB), Bangkok, Thailand, (S16-1-S16-9). 03-05 October 2012. doi:10.1186/1471-2105-13-S17-S16

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Author Srihari, Sriganesh
Leong, Hon Wai
Title of paper Temporal dynamics of protein complexes in PPI Networks: a case study using yeast cell cycle dynamics
Conference name Asia Pacific Bioinformatics Network (APBioNet) 11th International Conference on Bioinformatics (InCoB)
Conference location Bangkok, Thailand
Conference dates 03-05 October 2012
Proceedings title Proceedings of Asia Pacific Bioinformatics Network (APBioNet) 11th International Conference on Bioinformatics (InCoB)   Check publisher's open access policy
Journal name BMC Bioniformatics   Check publisher's open access policy
Place of Publication London, United Kingdom
Publisher BioMed Central
Publication Year 2012
Sub-type Fully published paper
DOI 10.1186/1471-2105-13-S17-S16
Open Access Status DOI
ISSN 1471-2105
Volume 13
Issue Suppl. 17
Start page S16-1
End page S16-9
Total pages 9
Collection year 2013
Language eng
Formatted Abstract/Summary
Complexes of physically interacting proteins are one of the fundamental functional units responsible for driving key biological mechanisms within the cell. With the advent of high-throughput techniques, significant amount of protein interaction (PPI) data has been catalogued for organisms such as yeast, which has in turn fueled
computational methods for systematic identification and study of protein complexes. However, many complexes are dynamic entities - their subunits are known to assemble at a particular cellular space and time to perform a particular function and disassemble after that - and while current computational analyses have concentrated on studying the dynamics of individual or pairs of proteins in PPI networks, a crucial aspect overlooked is the dynamics of whole complex formations. In this work, using yeast as our model, we incorporate ‘time’ in the form of cell-cycle phases into the prediction of complexes from PPI networks and study the temporal phenomena of
complex assembly and disassembly across phases. We hypothesize that ‘staticness’ (constitutive expression) of proteins might be related to their temporal “reusability” across complexes, and test this hypothesis using complexes predicted from large-scale PPI networks across the yeast cell cycle phases. Our results hint towards a biological design principle underlying cellular mechanisms - cells maintain generic proteins as ‘static’ to enable their “reusability” across multiple temporal complexes. We also demonstrate that these findings provide additional support and alternative explanations to findings from existing works on the dynamics in PPI networks.
Keyword Saccharomyces Cerevisiae
Interactome
Database
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

 
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