The most rightward and upward shifted cells within each of these populations have been reported to be enriched in colony-forming cell (CFC) comprising alveolar progenitors and multipotent mammary repopulating units (MRUs), respectively [27].
Hence, contrary to transcriptomics microarray data, where low log-ratio values are meaningful as long as the differences between conditions are statistically significant, when interpreting ChIP-on-chip and DNA methylation microarray data, the upper quantile is of most interest, as it generally comprises mostly enriched probes.
For the TOG genes, only three gene groups were enriched comprising sterol, cholesterol and lipid biosynthesis.
Histones comprised a significantly enriched category in the GO enrichment analysis of genes that increased when comparing M4 and M5 while decreasing in M5 M6 and in super-clusters with a peak in M5.
In contrast, the monocyte-specific functional signature comprised ribosomal genes enriched in ribosomal-related functions, such as translational elongation.
Cluster 2, comprising 23 proteins, is enriched with terms relating to oxidation reduction process.
The ubiquitin-mediated proteolysis pathway was the most significantly enriched pathway, comprising 10% of the significant intermediators.
Additionally we compared our RING1B peak data with previously published data for RING1B and H3K27me3 (Ku et al., 2008 ), comprising approximately 1,500 significantly enriched genomic sites for RING1B that in large part overlapped with H3K27me3 peaks.
After acclimatization, the animals were fed, under the same holding conditions for an additional four weeks, either a low cholesterol (normal) diet (0.03%, Dyets Inc., Bethlehem, PA, USA) or a high cholesterol diet (Dyets Inc ., comprising an identical chow enriched with 1% cholesterol by weight.
Some functionally enriched modules comprised of these SVV-significant proteins are discussed in the following sections.
