Table 1 contains the 10 most significant gene set hits calculated by FDR-FET using reference set option 1 (ie, "genes") and maximal FDR at 35%.
The membrane metalloendopeptidase gene (MME), was the most significant gene with nominal P value of 2.5 × 10−5, which survived Bonferroni correction for multiple testing (P = 0.019).
The most significant gene expression among them was that of ferritin genes, as the availability of Fe in cells would be deduced from the expression change of ferritin genes.
In order to make the search more specific, only the most significant gene targets were taken into consideration.
Within the top ten most significant gene set overlaps, multiple functional categories associated with development were strongly enriched within our differentially methylated gene list.
Interestingly ADORA1 was the most significant gene differentially expressed between EAT and MAT, but also the gene more highly linked to cardiovascular diseases in IPA.
The most significant gene pathways that distinguish SF and SC fibrocytes include the immune and inflammatory response, chemotaxis, RNA processing and lipid metabolism pathways.
The most significant gene network (p = 10−35) is involved in cellular growth and has as central nodes the following molecules: BCL3, JNK, insulin, p38 MAPK, MBP, PKC, NFκB, ERK, MAPK and CCR5 (Figure 1C).
Among the most significant gene expression changes are the downregulation of c-Myc and the upregulation of THBS1 and CTSD, all of which change by more than 1000 RPM and greater than 20×.
In contrast, the most significant gene set that was up-regulated by SRA overexpression is TNFALPHA_ADIP_DN; i.e., SRA induced genes that are repressed by TNFα in this gene set (Figure 8B and Table S6).
It is also interesting that the miR27 family showed up as one of the most significant gene sets in this particular analysis given the known role of this miRNA in cellular proliferation.
