Fig. 3
Comparison of HTRgene results to known biological pathways for cold and heat stress. The known cold and heat stress pathway are organized into signal transmission, TF cascade, and downstream gene level pathways. a Cold stress analysis. In the signal transmission level pathway, the cold stress signal sequentially activate stress response signaling proteins, such as CBL-CIPKs, CPKs, CLRK, MEKK1, MKK2, MPK3/4/6, CAMTA3, and ICE1 [27, 29]. In the TF cascade level pathway, CAMTA3 and ICE1 bind to MYB, CG1, and ICE1-box DNA cis-elements and initiate gene expression regulation of (DREB)/C-repeat binding factor (CBF) family including CBF1/DREB1B, CBF2/DREB1C, and CBF3/ DREB1A, respectively [28]. The HTRgene analysis result, CBFs that are known as “master switches” of the cold acclimation response [34] bind to CRT/DRE elements [35–37] and regulate many downstream genes that confer chilling and freezing tolerance to plants. The HTRgene analysis result included CBF1, CBF2, and CBF3 in the second response phase clusters “p2,” and the 21 donwstream genes of CBFs in the later phase clusters “p4,” “p6,” “p7,” “p8,” “p9,” “p10,” “p11,” and “p12.” b Heat stress analysis. In the signal transmission level pathway, the heat stress sequentially activates stress response signaling proteins, such as CBL-CIPKs, CPKs, PP7, CDKA1, CBK3, and HSFA1s [38]. In the heat stress TF cascade level pathway, HSFA1s that are the major regulators [45] of heat stress response initiate gene expression regulation of heat shock responsive TFs: HSFB1A, HSFB2A, HSFB2B, HSFA2, and HSFA7A, [38]. Then, transcriptional upregulation is accelerated in a feed-forward fashion that HSFBs, HSFA7A, and HSFA2 bind to HSE elements and up-regulate themselves again [46]. In the downstream level pathway, the heat shock factor TFs regulate the heat stress responsive downstream genes [47–49]. The HTRgene analysis assigned heat shock factors, HSFA2, HSFA7A, and HSFBs, to the second response phase “p2.” and the 52 downstream genes of the heat shock factors to the later response phases, “p2,” “p3,” “p4,” “p5,” “p6,” and “p7.”