Entrez ID designations, assigned to the array probes by Illumina, were uploaded to the Innate DB database and a Gene Ontology (GO) over-representation analysis was performed for gene groups signifying a particular molecular function or biological process, or occurring in specific cellular compartments (Lynn et al., 2008).
However, such methods were limited by being laborious or requiring that the array probes were capable of defining polymorphism between strains.
A possible explanation for their abundance is that random species of sample DNA non-specifically anneal to the single stranded DNA hybridized to the array probe by the primer, which in our case is 57 bp.
In total 1,654 82.744%) of the 1,999 MPH-correlated genes were unambiguously localized on the B73 genome by mapping and filtering analysis of the array probe sequences.
Primers and TaqMan probes (Additional file 1) were designed with the Primer Express software (Applied Biosystems, Foster City, CA) using pig sequences obtained by performing a BLAST search with the array probe sequence.
Second, in the case of the variable loci reported by a single probe in the oligonucleotide arrays (Table 2), it was not always possible to design the MLPA probes in the exact same place, and they were designed within one kb around the array probe.
Validation experiments, using BS-pyrosequencing, confirmed the differential methylation at SREBF1 and LDLR between the experimental groups at the CpG sites defined by the methylation array probes.
Of our 2673 probesets, only 27% had corresponding probesets on the Plus 2.0 array through mapping to common exonic locus, such that the Plus 2.0 array probesets identified are contained within or overlapping the genomic regions spanned by the Exon array probes (see Supplementary Methods for more details).
