Analyzing the Cytoskeletal Transcriptome: Sex Differences in Rat Hypothalamus
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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.
