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

Frontiers in Cellular Neuroscience
Justin BalsorKathryn M Murphy

Abstract

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 ...Continue Reading

References

Aug 1, 1985·The Journal of Medicine and Philosophy·M J Flower
Dec 22, 1985·The Journal of Comparative Neurology·M B Luskin, C J Shatz
Nov 1, 1965·Journal of Neurophysiology·T N Wiesel, D H Hubel
Oct 27, 1999·Proceedings of the National Academy of Sciences of the United States of America·E M QuinlanM F Bear
Mar 16, 2004·Science·Michela FagioliniTakao K Hensch
Apr 20, 2004·The European Journal of Neuroscience·Lieselotte CnopsLutgarde Arckens
Jun 26, 2004·Annual Review of Neuroscience·Takao K Hensch
Mar 18, 2005·Developmental Psychobiology·Kathryn M MurphyDavid G Jones
Apr 27, 2005·Journal of Bioinformatics and Computational Biology·Chris Ding, Hanchuan Peng
Nov 2, 2005·Nature Reviews. Neuroscience·Takao K Hensch
Apr 4, 2006·Nature Neuroscience·Marta Majdan, Carla J Shatz
Aug 12, 2006·Proceedings of the National Academy of Sciences of the United States of America·Ratan D BhardwajJonas Frisén
Aug 19, 2006·Science·Pasko Rakic
Feb 14, 2007·Neuron·Benjamin D PhilpotMark F Bear
Jan 19, 2008·Trends in Neurosciences·Benjamin J Hall, Anirvan Ghosh
Apr 9, 2008·Progress in Brain Research·Arianna Maffei, Gina Turrigiano
Apr 19, 2008·Science·José Fernando Maya VetencourtLamberto Maffei
Nov 4, 2008·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Gordon B SmithMark F Bear
Mar 12, 2009·Proceedings of the National Academy of Sciences of the United States of America·Kathleen K A ChoMark F Bear
May 22, 2009·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Melanie A GaineyGina G Turrigiano
Jun 19, 2010·Frontiers in Aging Neuroscience·Kate WilliamsKathryn M Murphy
Jul 2, 2010·Frontiers in Cellular Neuroscience·Joshua G A PintoKathryn M Murphy
Oct 29, 2010·Journal of Anatomy·Gavin ClowryPasko Rakic
Mar 15, 2011·Molecular & Cellular Proteomics : MCP·Martijn DahlhausChristiaan N Levelt
Jan 1, 2010·Frontiers in Synaptic Neuroscience·Rylan S LarsenBenjamin D Philpot
Jan 1, 2010·Frontiers in Synaptic Neuroscience·Brett R BestonKathryn M Murphy
Aug 10, 2011·Neural Plasticity·J Alexander HeimelChristiaan N Levelt
Apr 3, 2012·Annual Review of Neuroscience·Christiaan N Levelt, Mark Hübener
Apr 20, 2012·The European Journal of Neuroscience·Sajjida JafferFrank Sengpiel
Feb 19, 2013·Current Biology : CB·Kevin R Duffy, Donald E Mitchell
May 17, 2013·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Mary E Lambo, Gina G Turrigiano
Dec 4, 2013·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Sam F Cooke, Mark F Bear

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Methods Mentioned

BETA
PCA
protein measurements

Software Mentioned

Visual Neuroscience Lab Open Science Framework ( OSF )
hclust
fviz
ggarrange
Rtsne
Rat
NewFeatures
pca
Synaptic Gene Ontologies ( SynGO )
R package PlasticityPhenotypes

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