The expression of K8 and K18 RNAs appear coordinately regulated (Figure 1C).
Moreover, we observed that the differential expression of COX-2/PTGS2 between A17 and BB1 cells was epigenetically regulated (Figure S1).
The TCA cycle is central to energy metabolism and here we were surprised to find that its genes are not uniformly transcriptionally regulated (Figure 3a).
Although coordinated expressions were detected for a small subset of the loci, majority of the sense and antisense transcripts tend to be independently regulated (Figure 3C).
When we examined the conservation of binding sites within 5 kb of the TSS of PPARγ regulated vs. non-regulated genes, we found a significant enrichment of conserved heterosites with upregulated genes (65% upregulated vs. 42% down regulated, Figure S5).
Only unregulated nodes (proteins) that are connected to two or more regulated partners were kept to generate a network where all the end nodes are differentially regulated (Figure 4B).
Genes encoding proteins involved in metabolism and cellular process are among the most up regulated genes, and those encoding proteins involved in membrane transport are among the most down regulated (Figure 1).
Following L. donovani infection, the phosphorylation of p38 MAPK was down regulated (Figure 5B) which remained unchanged in the presence of an inhibitor of p38 MAPK (SB203580, data not shown).
The IgG4 heritability estimates were highest of all isotypes and subclasses, with h2 values being above 0.5 for responses to all antigens by the child twins in both dry and wet seasons, indicating that IgG4 responses are most strongly genetically regulated (Figure 1).
By selecting genes with the most drastic changes in level of expression (fold change in log2 > 2 or <−2), we were able to define a signature of 20 genes for influenza A virus infection with similar amounts of those up and down regulated (Figure 5A, Table 1).
In addition to the staminodia-specific up-regulation of 160 genes, there are 197 genes co-up-regulated with carpels and 124 genes co-up-regulated with stamens while stamens and carpels have 142 genes co-up-regulated (Figure 2C).
