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Abstract
Gene duplication is a fundamental evolutionary mechanism that contributes to biological complexity and diversity. Traditionally, research has focused on the duplication of gene sequences. However, evidence suggests that the duplication of regulatory elements may also play a significant role in the evolution of genomic functions. This doctoral dissertation observes the evolution of regulatory relationships belonging to gene-family-specific substructures in a GRN under gene duplication.
A gene duplication model is used to carry out the observations. 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 selected gene are retained through duplication is determined by a vector of probabilities. That is to say that each gene family has its own retention probability.
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. 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 is when all regulatory links are inherited at each duplication step and partial duplication is when regulation inheritance varies at each duplication step. Note that full duplication is just a special case of partial duplication. Moments for the number of occurrences of subnetwork motifs is determined in each model. In the end, the results presented offer a method for discovering gene-family-specific substructures that are significant in a GRN under gene duplication.
A gene duplication model is used to carry out the observations. 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 selected gene are retained through duplication is determined by a vector of probabilities. That is to say that each gene family has its own retention probability.
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. 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 is when all regulatory links are inherited at each duplication step and partial duplication is when regulation inheritance varies at each duplication step. Note that full duplication is just a special case of partial duplication. Moments for the number of occurrences of subnetwork motifs is determined in each model. In the end, the results presented offer a method for discovering gene-family-specific substructures that are significant in a GRN under gene duplication.