Analyzing the Cytoskeletal Transcriptome: Sex Differences in Rat Hypothalamus

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.