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Susanne Marie Cardwell,
Administrative Coordinator for Genome Alberta

    While flipping through notes on the recent Applied Computational Genomics Course I stumbled upon an interesting concept that as a Communications graduate student found quite remarkable: the coming advent of 3- and 4-dimensional annotation.  As I started out at the University of Calgary as an Honours Mathematics major, I found some interesting parallels with the multi-dimensional annotation and the concept of multiple (spatial) dimensions in mathematics.
    
    1-dimensional and 2-dimensional genome annotation have been areas researched and studied for quite some time, and will continue to have a formative role in genetics research, as they provide unique information, becoming more complex with each layer of dimensionality.
    
    Like a point on a line, one dimensional annotation provides information on location, but does not give information about spatial or evolutionary organization that can be found in higher dimensional annotations. In mathematics, the one-dimensionality can be likened to investigating a point on a line, which demonstrates position; the two-dimensionality provides information on a region in a graph, which allows for organization of gene structures, positioning, and relationships to become more apparent. Three-dimensionality, allows for information on more than a surface, but an object within a x, y, z plane system, which enables the concept of derivatives and integrals, from a mathematical sense, to perform operations and to include more complex functions such as motion and transformation from one dimensionality to another.

    As my fascination with the multiple dimensionality of annotation grew, I went to Nature Reviews and gleaned, from a genetics research amateur’s perspective, some more information.

    A new wave of research is coming to the fore –  namely, three dimensional annotation. Three-dimensional annotation analyzes the spatial positioning of genes within the x, y, z plane formation of the cell itself, allowing for the organizational structure of genes within the cell to be characterized and assessed. Four-dimensional annotation is expected to be able to capture both lifespan gene activity profiles and longer term adaptive evolutionary time variations in the genome sequence, which brings in the concept of time (and evolutionary change and motion) into the notion of the fourth dimension. This advanced annotation of genomes will allow for their functional characteristics to be more readily accessible. 

    2-dimensional annotations are the current mode of annotation, and provide information that enables modeling of transformations, but does not provide information on the arrangements or expression (i.e. translation to protein over time) of genes in a three-dimensional space. It appears that the higher dimensionality of annotation will begin to capture this along with the evolution of genes. 

    Software for visualization of 3-dimensionality in genetic structures is currently available, and will likely be an integral component of 3-dimensional annotation, although current 2-dimensional graphics enable 3-dimensional annotation. 

    As we develop more comprehensive information on 3-dimensional genetic structures, the structural organization of genes within the cell, and the adaptive evolution of gene structures, this information will aid in understanding of genes and the capacity to modify or replicate cell behavior. Bioinformatics software will adjust for this multiple dimensionality in visualization tools.

Perhaps with greater emphasis on viewing genome multi-dimensionality, our understanding of the genome in a cell will become even more dynamic as its layers of complexity become unfolded.