{"title":"Counting Subnetworks Under Gene Duplication in Genetic Regulatory Networks","authors":"Ashley Scruse, Jonathan Arnold, Robert Robinson","doi":"arxiv-2405.03148","DOIUrl":null,"url":null,"abstract":"Gene duplication is a fundamental evolutionary mechanism that contributes to\nbiological complexity and diversity (Fortna et al., 2004). Traditionally,\nresearch has focused on the duplication of gene sequences (Zhang, 1914).\nHowever, evidence suggests that the duplication of regulatory elements may also\nplay a significant role in the evolution of genomic functions (Teichmann and\nBabu, 2004; Hallin and Landry, 2019). In this work, the evolution of regulatory\nrelationships belonging to gene-specific-substructures in a GRN are modeled. In\nthe model, a network grows from an initial configuration by repeatedly choosing\na random gene to duplicate. The likelihood that the regulatory relationships\nassociated with the selected gene are retained through duplication is\ndetermined by a vector of probabilities. Occurrences of gene-family-specific\nsubstructures are counted under the gene duplication model. In this thesis,\ngene-family-specific substructures are referred to as subnetwork motifs. These\nsubnetwork motifs are motivated by network motifs which are patterns of\ninterconnections that recur more often in a specialized network than in a\nrandom network (Milo et al., 2002). Subnetwork motifs differ from network\nmotifs in the way that subnetwork motifs are instances of gene-family-specific\nsubstructures while network motifs are isomorphic substructures. These\nsubnetwork motifs are counted under Full and Partial Duplication, which differ\nin the way in which regulation relationships are inherited. Full duplication\noccurs when all regulatory links are inherited at each duplication step, and\nPartial Duplication occurs when regulation inheritance varies at each\nduplication step. Moments for the number of occurrences of subnetwork motifs\nare determined in each model. The results presented offer a method for\ndiscovering subnetwork motifs that are significant in a GRN under gene\nduplication.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"19 1","pages":""},"PeriodicalIF":0.0000,"publicationDate":"2024-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"arXiv - QuanBio - Molecular Networks","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/arxiv-2405.03148","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
Abstract
Gene duplication is a fundamental evolutionary mechanism that contributes to
biological complexity and diversity (Fortna et al., 2004). Traditionally,
research has focused on the duplication of gene sequences (Zhang, 1914).
However, evidence suggests that the duplication of regulatory elements may also
play a significant role in the evolution of genomic functions (Teichmann and
Babu, 2004; Hallin and Landry, 2019). In this work, the evolution of regulatory
relationships belonging to gene-specific-substructures in a GRN are modeled. In
the model, a network grows from an initial configuration by repeatedly choosing
a random gene to duplicate. The likelihood that the regulatory relationships
associated with the selected gene are retained through duplication is
determined by a vector of probabilities. Occurrences of gene-family-specific
substructures are counted under the gene duplication model. In this thesis,
gene-family-specific substructures are referred to as subnetwork motifs. These
subnetwork motifs are motivated by network motifs which are patterns of
interconnections that recur more often in a specialized network than in a
random network (Milo et al., 2002). Subnetwork motifs differ from network
motifs in the way that subnetwork motifs are instances of gene-family-specific
substructures while network motifs are isomorphic substructures. These
subnetwork motifs are counted under Full and Partial Duplication, which differ
in the way in which regulation relationships are inherited. Full duplication
occurs when all regulatory links are inherited at each duplication step, and
Partial Duplication occurs when regulation inheritance varies at each
duplication step. Moments for the number of occurrences of subnetwork motifs
are determined in each model. The results presented offer a method for
discovering subnetwork motifs that are significant in a GRN under gene
duplication.