Nine hybridisations between a single pig skeletal muscle RNA sample and three human cDNA nylon microarrays were completed.
Network analysis of the microarray data was completed using the Ingenuity Pathway Analysis software [ 50].
Quality assurance of microarray data was completed using the affyQAReport function from the Bioconductor package affyQCReport.
MiRNA microarray analysis was completed by searching the TargetScan database for mRNAs, which were targeted by the differently regulated miRNAs.
Tissue microarray construction was completed in the Liver Cancer Institute of Zhongshan Hospital with clinical HCC specimens obtained from a cohort of 48 patients.
Microarray hybridization and analysis was completed at the University of North Carolina at Chapel Hill Functional Genomics Core Facility.
To further validate our microarray data, regression analysis was completed for the two data sets.
Once data generation for the validation cohort was completed, the expression microarray signal intensity data from all individuals and all time points in that cohort were processed in a single batch.
These assays were done after the microarray analyses were completed, at which time RNA samples were available from 8 men and 7 women.
