Both in utero (using embryonic heart tissues) and in vitro (using iPSCs and differentiated cells) microarray datasets were deposited to the NCBI Gene Expression Omnibus (GEO) database.
We did not analyse the dataset differentiated by migraine, tension-type headache, pMOH and other headaches or differentiated by anxiety alone, depression alone or anxiety and depression, because the subgroups would have been too small.
Analysis of the genomic data in the context of gene ontology, by Ingenuity Pathway Analysis (IPA), allowed us to ascribe biological functional networks to the differentiated transcript abundance dataset.
In addition, CCA can have a high sensitivity for identifying the differentiated cells in a dataset that are similar to the ones in another dataset.
We then used Significant B test to distinguish the most differentiated proteins in each dataset (P < 0.05 according to Significance B test) [ 18].
Because the primary diagnosis and any secondary diagnoses were not differentiated in the BioSense dataset we received, we used a convention to define the primary diagnosis.
The differences in relative abundance of clonal complexes were mirrored by F ST values calculated from concatenated nucleotide sequences of the MLST loci, which indicated that the Australian dataset was 3.6% differentiated and the Curaçao set 9.9% differentiated from the Oxfordshire dataset.
Two mouse PPARγ datasets, one from differentiated adipocytes and one from resting MФ are currently available [ 38, 39].
Next, we calculated measures of polymorphism and human chimpanzee divergence for all five-gene datasets and five differentiated genomic regions (fig. 1 and supplementary table S6, Supplementary Material online): CDS, introns, promoters, CNC, and UTRs.
The gene expression dataset of C2C12 cells differentiated in vitro was retrieved from NCBI GEO [ 33]; dataset accession number GDS2412 [ 13].
