The regression model consisted of a set of 5 regressors (instruction, non-regulated negative, non-regulated neutral, regulated negative, regulated neutral) convolved with the hemodynamic response function and six regressors describing residual motion.
The result indicates that cool-season turfgrass and forage grass may have more negative regulated genes compared with positive regulation ones in the heat stress response pathway.
On the contrary, auxin and gibberellin-related genes, regulating the growing and differentiation of the tissues, are negative regulated during the abscission induction.
Since miRNAs act as negative regulators, up-regulated miRNAs resulted in down-regulated target mRNAs, and vice versa.
As highlighted in Figure 1, the single most significant and one of the most fold-changed discriminant genes is DNA-damage inducible transcript 4 (Ddit4), a p53-regulated negative regulator of the Frap1 pathway [27], which is increased by CR by over 33-fold (80.1-fold as measured by Q-RT-PCR).
In pre-adipocytes, positive regulators tended to be down-regulated upon ZEB1 KD while negative regulators were up-regulated (p = 0.007, Wilcoxon rank-sum test comparing fold-changes), suggesting that ZEB1 acts primarily as a positive regulator in the context of the aGRN, consistent with observations from our phenotype-profiling experiments.
Of interest, genes involved in cAMP mediated signaling and calcium regulation such as Pde4b (7.22 fold), Calcr (6.14 fold), and Sstr2 (11.4 fold) were all up-regulated, while negative regulator of GPCR signaling such as Gprasp1 (59.82 fold), and Rgs3 (5.14 fold) [ 38] were down-regulated.
We found that differentially expressed genes were significantly enriched in the GO categories, including positive regulation of cell proliferation for up-regulated genes and negative regulation of cell proliferation for down-regulated genes.
PP2C phosphatases are negative regulators of stress-regulated signalling mediated by PKA and the p38 and JNK MAPK pathways [ 93, 94] in mammals.
Two genes involved in signal transduction (STMN1, CDC25B), which code for proteins of the MAP kinase pathway (MAPK), were up-regulated, while a negative regulator of this pathway (DUSP2) was down-regulated in challenged animals at 12 MPC.
The number represents the log2-ratio or fold change for positive (up-regulated) and negative (down-regulated) genes Regulation patterns of transcriptome sequencing were in accordance to quantitative real time (qRT) PCR experiments applied to selected genes in order to verify the expression data obtained by the RNA-Seq approach (Additional file 2: Table S1).
