ArticleBMC bioinformatics2012
Temporal dynamics of protein complexes in PPI networks: a case study using yeast cell cycle dynamics.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Article
- The High Ratio of the Plasma miR-96/miR-99b Correlated With Poor Prognosis in Patients With Metastatic Colorectal Cancer.Frontiers in molecular biosciences · 2021Article
- DPCT: A Dynamic Method for Detecting Protein Complexes From TAP-Aware Weighted PPI Network.Frontiers in genetics · 2020Article
- Detecting complexes from edge-weighted PPI networks via genes expression analysis.BMC systems biology · 2018Article
- Mapping biological process relationships and disease perturbations within a pathway network.NPJ systems biology and applications · 2018Article
- iOPTICS-GSO for identifying protein complexes from dynamic PPI networks.BMC medical genomics · 2017Article
- An uncertain model-based approach for identifying dynamic protein complexes in uncertain protein-protein interaction networks.BMC genomics · 2017Article
- RNA-seq based gene expression analysis of ovarian granulosa cells exposed to zearalenoneOncotarget · 2017Article
- Identification of hub genes involved in the development of hepatocellular carcinoma by transcriptome sequencing.Oncotarget · 2017Article
- Development of an in silico method for the identification of subcomplexes involved in the biogenesis of multiprotein complexes in Saccharomyces cerevisiae.BMC systems biology · 2017Article
- BiCAMWI: A Genetic-Based Biclustering Algorithm for Detecting Dynamic Protein Complexes.PloS one · 2016Article
- Mining Temporal Protein Complex Based on the Dynamic PIN Weighted with Connected Affinity and Gene Co-Expression.PloS one · 2016Article
- Time dynamics of protein complexes in the AD11 transgenic mouse model for Alzheimer's disease like pathology.BMC neuroscience · 2015Article
- Temporal Identification of Dysregulated Genes and Pathways in Clear Cell Renal Cell Carcinoma Based on Systematic Tracking of Disrupted Modules.Computational and mathematical methods in medicine · 2015Article
- Detecting temporal protein complexes from dynamic protein-protein interaction networks.BMC bioinformatics · 2014Article
- Identifying dynamic protein complexes based on gene expression profiles and PPI networks.BioMed research international · 2014Article
- Complex-based analysis of dysregulated cellular processes in cancer.BMC systems biology · 2014Article
- Investigation of the hub genes and related mechanism in ovarian cancer via bioinformatics analysis.Journal of ovarian research · 2013Article
- Identifying conserved protein complexes between species by constructing interolog networks.BMC bioinformatics · 2013Article
- InCoB2012 Conference: from biological data to knowledge to technological breakthroughs.BMC bioinformatics · 2012Article
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2 authors.
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Abstract
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.
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