ArticleGenome biology2015
An approach for determining and measuring network hierarchy applied to comparing the phosphorylome and the regulome.
Article in Genome biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed.
- LysG-driven transcriptional network rewiring underlies lineage-specific phenotypes in Mycobacterium tuberculosis.Nature communications · 2026Article
- Representing core gene expression activity relationships using the latent structure implicit in Bayesian networks.Bioinformatics (Oxford, England) · 2024Article
- iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease.PLoS computational biology · 2023Article
- Single-cell network biology characterizes cell type gene regulation for drug repurposing and phenotype prediction in Alzheimer's disease.PLoS computational biology · 2022Article
- Graph hierarchy: a novel framework to analyse hierarchical structures in complex networks.Scientific reports · 2021Article
- Observational
- Integrative inference of transcriptional networks in Arabidopsis yields novel ROS signalling regulators.Nature plants · 2021Article
- Plants are intelligent, here's how.Annals of botany · 2020Article
- Article
- Hierarchical cooperation of transcription factors from integration analysis of DNA sequences, ChIP-Seq and ChIA-PET data.BMC genomics · 2019Article
- A network of epigenomic and transcriptional cooperation encompassing an epigenomic master regulator in cancer.NPJ systems biology and applications · 2018Article
- Delineating functional principles of the bow tie structure of a kinase-phosphatase network in the budding yeast.BMC systems biology · 2017Article
- Understanding Physiology in the Continuum: Integration of Information from Multiple -Frontiers in pharmacology · 2017Article
- Integrative analysis of cancer genes in a functional interactome.Scientific reports · 2016Article
- Reconstruction and topological characterization of the sigma factor regulatory network of Mycobacterium tuberculosis.Nature communications · 2016Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Many biological networks naturally form a hierarchy with a preponderance of downward information flow. In this study, we define a score to quantify the degree of hierarchy in a network and develop a simulated-annealing algorithm to maximize the hierarchical score globally over a network. We apply our algorithm to determine the hierarchical structure of the phosphorylome in detail and investigate the correlation between its hierarchy and kinase properties. We also compare it to the regulatory network, finding that the phosphorylome is more hierarchical than the regulome.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.