ArticlePLoS computational biology2011
Modification of gene duplicability during the evolution of protein interaction network.
Article in PLoS computational biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 49 citations in OpenAlex.
- A temporal gradient of cytonuclear coordination of chaperonins and chaperones during RuBisCo biogenesis in allopolyploid plants.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Functional compensation of mouse duplicates by their paralogs expressed in the same tissues.Genome biology and evolution · 2022Article
- Comparative assessment of genes driving cancer and somatic evolution in non-cancer tissues: an update of the Network of Cancer Genes (NCG) resource.Genome biology · 2022Review
- Three topological features of regulatory networks control life-essential and specialized subsystems.Scientific reports · 2021Article
- The impact of whole genome duplications on the human gene regulatory networks.PLoS computational biology · 2021Article
- Pan-cancer detection of driver genes at the single-patient resolution.Genome medicine · 2021Article
- The Evolution of Gene Duplicates in Angiosperms and the Impact of Protein-Protein Interactions and the Mechanism of Duplication.Genome biology and evolution · 2019Article
- Membrane protein-regulated networks across human cancers.Nature communications · 2019Article
- Patient-specific cancer genes contribute to recurrently perturbed pathways and establish therapeutic vulnerabilities in esophageal adenocarcinoma.Nature communications · 2019Article
- The Network of Cancer Genes (NCG): a comprehensive catalogue of known and candidate cancer genes from cancer sequencing screens.Genome biology · 2019Article
- Modelling the evolution of transcription factor binding preferences in complex eukaryotes.Scientific reports · 2017Article
- Intrinsic protein disorder reduces small-scale gene duplicability.DNA research : an international journal for rapid publication of reports on genes and genomes · 2017Article
- Gene Duplicability of Core Genes Is Highly Consistent across All Angiosperms.The Plant cell · 2016Article
- NCG 5.0: updates of a manually curated repository of cancer genes and associated properties from cancer mutational screenings.Nucleic acids research · 2016Article
- Extracting functional trends from whole genome duplication events using comparative genomics.Biological procedures online · 2016Review
- Module organization and variance in protein-protein interaction networks.Scientific reports · 2015Article
- Article
- The role of the interactome in the maintenance of deleterious variability in human populations.Molecular systems biology · 2014Article
- Relationship between gene duplicability and diversifiability in the topology of biochemical networks.BMC genomics · 2014Article
- Dry computational approaches for wet medical problems.Journal of translational medicine · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Duplications of genes encoding highly connected and essential proteins are selected against in several species but not in human, where duplicated genes encode highly connected proteins. To understand when and how gene duplicability changed in evolution, we compare gene and network properties in four species (Escherichia coli, yeast, fly, and human) that are representative of the increase in evolutionary complexity, defined as progressive growth in the number of genes, cells, and cell types. We find that the origin and conservation of a gene significantly correlates with the properties of the encoded protein in the protein-protein interaction network. All four species preserve a core of singleton and central hubs that originated early in evolution, are highly conserved, and accomplish basic biological functions. Another group of hubs appeared in metazoans and duplicated in vertebrates, mostly through vertebrate-specific whole genome duplication. Such recent and duplicated hubs are frequently targets of microRNAs and show tissue-selective expression, suggesting that these are alternative mechanisms to control their dosage. Our study shows how networks modified during evolution and contributes to explaining the occurrence of somatic genetic diseases, such as cancer, in terms of network perturbations.
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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.