ArticlePLoS computational biology2021
The impact of whole genome duplications on the human gene regulatory networks.
Article in PLoS computational biology, 2021. 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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Who cites it
15 citing papers in PubMed, 30 citations in OpenAlex.
- Evolutionary study of oncogenes and tumor suppressor genes in breast carcinoma.Journal of Taibah University Medical Sciences · 2026Article
- Developmental contexts of gene-regulatory evolution following whole genome duplication in salmonids.Nature ecology & evolution · 2026Article
- Dynamic and non-additive gene regulation shapes maize responses to simultaneous salt and cold stress.Functional & integrative genomics · 2026Article
- Retinoid-X receptor action and disruption in development.Developmental biology · 2026Review
- The Evolutionary Flexibility of the Drosophila Circadian Clock: Network Constraints or Adaptive Freedom?Genome biology and evolution · 2026Article
- Ohno-miRNAs: miRNA pairs derived from whole-genome duplication.PLoS computational biology · 2025Article
- Assessing the Impact of Whole Genome Duplication on Gene Expression and Regulation During Arachnid Development.Genome biology and evolution · 2025Article
- A global genetic interaction map of a human cell reveals conserved principles of genetic networks.bioRxiv : the preprint server for biology · 2025Article
- Inverse and ProportionalGenes · 2024Article
- The duplication of genomes and genetic networks and its potential for evolutionary adaptation and survival during environmental turmoil.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Molecular Evolution of Aryl Hydrocarbon Receptor Signaling Pathway Genes.Journal of molecular evolution · 2023Article
- Whole-genome Duplications and the Long-term Evolution of Gene Regulatory Networks in Angiosperms.Molecular biology and evolution · 2023Article
- Dosage balance acts as a time-dependent selective barrier to subfunctionalization.BMC ecology and evolution · 2023Article
- Review
- Promoter evolution of mammalian gene duplicates.BMC biology · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This work studies the effects of the two rounds of Whole Genome Duplication (WGD) at the origin of the vertebrate lineage on the architecture of the human gene regulatory networks. We integrate information on transcriptional regulation, miRNA regulation, and protein-protein interactions to comparatively analyse the role of WGD and Small Scale Duplications (SSD) in the structural properties of the resulting multilayer network. We show that complex network motifs, such as combinations of feed-forward loops and bifan arrays, deriving from WGD events are specifically enriched in the network. Pairs of WGD-derived proteins display a strong tendency to interact both with each other and with common partners and WGD-derived transcription factors play a prominent role in the retention of a strong regulatory redundancy. Combinatorial regulation and synergy between different regulatory layers are in general enhanced by duplication events, but the two types of duplications contribute in different ways. Overall, our findings suggest that the two WGD events played a substantial role in increasing the multi-layer complexity of the vertebrate regulatory network by enhancing its combinatorial organization, with potential consequences on its overall robustness and ability to perform high-level functions like signal integration and noise control. Lastly, we discuss in detail the RAR/RXR pathway as an illustrative example of the evolutionary impact of WGD duplications in human.
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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.