Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks

Anthony Szedlak, Nicholas Smith, Li Liu, Giovanni Paternostro, Carlo Piermarocchi

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

The diverse, specialized genes present in today’s lifeforms evolved from a common core of ancient, elementary genes. However, these genes did not evolve individually: gene expression is controlled by a complex network of interactions, and alterations in one gene may drive reciprocal changes in its proteins’ binding partners. Like many complex networks, these gene regulatory networks (GRNs) are composed of communities, or clusters of genes with relatively high connectivity. A deep understanding of the relationship between the evolutionary history of single genes and the topological properties of the underlying GRN is integral to evolutionary genetics. Here, we show that the topological properties of an acute myeloid leukemia GRN and a general human GRN are strongly coupled with its genes’ evolutionary properties. Slowly evolving (“cold”), old genes tend to interact with each other, as do rapidly evolving (“hot”), young genes. This naturally causes genes to segregate into community structures with relatively homogeneous evolutionary histories. We argue that gene duplication placed old, cold genes and communities at the center of the networks, and young, hot genes and communities at the periphery. We demonstrate this with single-node centrality measures and two new measures of efficiency, the set efficiency and the interset efficiency. We conclude that these methods for studying the relationships between a GRN’s community structures and its genes’ evolutionary properties provide new perspectives for understanding evolutionary genetics.

Original languageEnglish (US)
Article numbere1005009
JournalPLoS Computational Biology
Volume12
Issue number6
DOIs
StatePublished - Jun 1 2016

Fingerprint

Community Structure
Gene Regulatory Networks
Gene Regulatory Network
Topological Properties
community structure
Genes
Gene
gene
genes
Human
gene regulatory networks
Complex Networks
Complex networks
myeloid leukemia
history
Gene Duplication
protein binding
gene duplication
Multigene Family
multigene family

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Modeling and Simulation
  • Ecology
  • Molecular Biology
  • Genetics
  • Cellular and Molecular Neuroscience
  • Computational Theory and Mathematics

Cite this

Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks. / Szedlak, Anthony; Smith, Nicholas; Liu, Li; Paternostro, Giovanni; Piermarocchi, Carlo.

In: PLoS Computational Biology, Vol. 12, No. 6, e1005009, 01.06.2016.

Research output: Contribution to journalArticle

Szedlak, Anthony ; Smith, Nicholas ; Liu, Li ; Paternostro, Giovanni ; Piermarocchi, Carlo. / Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks. In: PLoS Computational Biology. 2016 ; Vol. 12, No. 6.
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