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The Cytoskeleton pp 119–134Cite as

Analyzing the Cytoskeletal Transcriptome: Sex Differences in Rat Hypothalamus

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Part of the book series: Neuromethods ((NM,volume 79))

Abstract

This chapter presents the protocol established in our laboratory to determine the cytoskeletal genomic fabric (CGF), defined as the most inter-coordinately and stably expressed gene web whose encoding proteins form the intracellular scaffolding. In addition to detailed experimental procedures and conventional bioinformatics, novel analytical tools are introduced to reveal hidden features of the cytoskeletal transcriptome. Thus, the Prominent Gene Analysis ranks CGF genes according to their contribution to fabric synchronous expression and robustness against variable conditions, Pair-Wise Relevance determines the fabric topology, and the “transcriptomic distance” quantifies fabric differences between conditions. The new tools use expanded transcriptomic quantifiers, considering not only the expression level but also the control and intercoordination of the fabric genes.

This method is here used to analyze the sex differences in rat hypothalamic CGF and the transcriptomic networks by which CGF and the myelination genomic fabric (MGF) modulate each other. The analysis revealed profound differences between the adult males and estrus-stage females in the CGF topology and CGF–MGF interaction that can provide a basis for the substantial sex dichotomy in neurodegenerative diseases.

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Acknowledgement

Dr. David C. Spray’s (Einstein) comments on biological interpretation of experimental data are gratefully acknowledged.

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Authors and Affiliations

  1. D.P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY, USA

    Sanda Iacobas, Genevieve Neal-Perry & Dumitru Andrei Iacobas

Authors
  1. Sanda Iacobas
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  2. Genevieve Neal-Perry
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  3. Dumitru Andrei Iacobas
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Corresponding author

Correspondence to Dumitru Andrei Iacobas .

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Editors and Affiliations

  1. Faculty of Medicine, Neuroanatomy & Molecular Brain Research, Ruhr-Universität Bochum, Universitätsstrasse 150, Bochum, 44801, Germany

    Rolf Dermietzel

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Iacobas, S., Neal-Perry, G., Iacobas, D.A. (2013). Analyzing the Cytoskeletal Transcriptome: Sex Differences in Rat Hypothalamus. In: Dermietzel, R. (eds) The Cytoskeleton. Neuromethods, vol 79. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-266-7_6

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  • DOI: https://doi.org/10.1007/978-1-62703-266-7_6

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-62703-265-0

  • Online ISBN: 978-1-62703-266-7

  • eBook Packages: Springer Protocols

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