ArticlePLoS computational biology2016
Evolutionary and Topological Properties of Genes and Community Structures in Human Gene Regulatory Networks.
Article in PLoS computational biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
5 citing papers in PubMed, 12 citations in OpenAlex.
- Topological benchmarking of algorithms to infer gene regulatory networks from single-cell RNA-seq data.Bioinformatics (Oxford, England) · 2024Article
- Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins.Genome biology · 2024Article
- Naturally occurring combinations of receptors from single cell transcriptomics in endothelial cells.Scientific reports · 2022Article
- A Transcriptome Community-and-Module Approach of the Human Mesoconnectome.Entropy (Basel, Switzerland) · 2021Article
- Cell cycle time series gene expression data encoded as cyclic attractors in Hopfield systems.PLoS computational biology · 2017Article
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Authors and funding
5 authors at 4 institutions in 1 country.
Funding
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.
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Registered trials
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