The Network Architecture of the Saccharomyces cerevisiae Genome

We propose a network-based approach for surmising the spatial organization of genomes from high-throughput interaction data. Our strategy is based on methods for inferring architectural features of networks. Specifically, we employ a community detection algorithm to partition networks of genomic int...

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Veröffentlicht in:PloS one Jg. 8; H. 12; S. e81972
Hauptverfasser: Hoang, Stephen A., Bekiranov, Stefan
Format: Journal Article
Sprache:Englisch
Veröffentlicht: United States Public Library of Science 09.12.2013
Public Library of Science (PLoS)
Schlagworte:
Algorithms
Analysis
Binding sites
Biochemistry
Cell Cycle Proteins - genetics
Cell Cycle Proteins - metabolism
Centromere - chemistry
Centromeres
Chromosomal Proteins, Non-Histone - genetics
Chromosomal Proteins, Non-Histone - metabolism
Clustering
Cohesin
Cohesins
Communities
Conformation
Datasets
Deoxyribonucleic acid
DNA
Gene expression
Gene Regulatory Networks
Genetic aspects
Genome, Fungal
Genomes
Genomics
Kinases
Network analysis
Networks
Partitions
Principles
Protein Interaction Mapping
RNA, Transfer - genetics
RNA, Transfer - metabolism
Saccharomyces cerevisiae
Saccharomyces cerevisiae - genetics
Saccharomyces cerevisiae - metabolism
Saccharomyces cerevisiae Proteins - genetics
Saccharomyces cerevisiae Proteins - metabolism
Telomerase
Telomere - chemistry
Telomeres
Yeast
United States > US
Virginia
ISSN:1932-6203, 1932-6203
Online-Zugang:Volltext
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Beschreibung
Zusammenfassung:We propose a network-based approach for surmising the spatial organization of genomes from high-throughput interaction data. Our strategy is based on methods for inferring architectural features of networks. Specifically, we employ a community detection algorithm to partition networks of genomic interactions. These community partitions represent an intuitive interpretation of genomic organization from interaction data. Furthermore, they are able to recapitulate known aspects of the spatial organization of the Saccharomyces cerevisiae genome, such as the rosette conformation of the genome, the clustering of centromeres, as well as tRNAs, and telomeres. We also demonstrate that simple architectural features of genomic interaction networks, such as cliques, can give meaningful insight into the functional role of the spatial organization of the genome. We show that there is a correlation between inter-chromosomal clique size and replication timing, as well as cohesin enrichment. Together, our network-based approach represents an effective and intuitive framework for interpreting high-throughput genomic interaction data. Importantly, there is a great potential for this strategy, given the rich literature and extensive set of existing tools in the field of network analysis.
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Competing Interests: The authors have declared that no competing interests exist.
Conceived and designed the experiments: SAH SB. Analyzed the data: SAH. Wrote the paper: SAH SB.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0081972