A Primer on Constructing Plasticity Phenotypes to Classify Experience-Dependent Development of the Visual Cortex

Many neural mechanisms regulate experience-dependent plasticity in the visual cortex (V1), and new techniques for quantifying large numbers of proteins or genes are transforming how plasticity is studied into the era of big data. With those large data sets comes the challenge of extracting biologically meaningful results about visual plasticity from data-driven analytical methods designed for high-dimensional data. In other areas of neuroscience, high-information content methodologies are revealing more subtle aspects of neural development and individual variations that give rise to a richer picture of brain disorders. We have developed an approach for studying V1 plasticity that takes advantage of the known functions of many synaptic proteins for regulating visual plasticity. We use that knowledge to rebrand protein measurements into plasticity features and combine those into a plasticity phenotype. Here, we provide a primer for analyzing experience-dependent plasticity in V1 using example R code to identify high-dimensional changes in a group of proteins. We describe using PCA to classify high-dimensional plasticity features and use them to construct a plasticity phenotype. In the examples, we show how to use this analytical framework to study and compare experience-dependent development and plasticity of V1 and apply the plasticity phenotype to translational research questions. We include an R package "PlasticityPhenotypes" that aggregates the coding packages and custom code written in RStudio to construct and analyze plasticity phenotypes.