From: Frequency-based time-series gene expression recomposition using PRIISM
Rank | Annotation | Comments | P Value (Treatment-Frequency Fold Change, 26 Hours) | Cold Upregulation Category*[54] |
---|---|---|---|---|
11 | AT1G02820: Late embryogenesis abundant 3 family protein/LEA3 family protein | LEA family proteins are associated with dehydration stress (and therefore cold) and general environmental stress in plants, and desiccation tolerance in other organisms including bacteria [60]. Cold response genes COR15A COR15B and COR47 are classified as LEA genes. Although not to the same degree as the COR genes, expression of this gene was upregulated by cold according to quantitative RT-PCR [60] | 3.29E-13 | Soil |
13 | AT2G23910: Cinnamoyl-CoA reductase-related | Implicated in the biosynthesis of phenylpropanoids [61, 62], which contribute to many different plant responses to biotic and abiotic stress/challenge [63] | 9.97E-13 | Plate |
23 | AT1G61800: GPT2 (Glucose-6-Phosphate Translocator 2) | A gpt2 mutant shows an impairment in photosynthetic acclimation in response to shifts to high irradiance light, which can be exacerbated under cold conditions [64] | 1.37E-09 | Plate |
29 | AT5G06760: Late embryogenesis abundant group 1 (LEA group 1) domain-containing protein | Similar to other LEA above (AT1G02820), expression of this gene is upregulated by cold according to quantitative RT-PCR [60] | 1.86E-08 | Soil |
37 | AT3G51240: F3H; TT6 (Flavanone 3-Hydroxylase; Transparent Testa 6) | Implicated in freezing stress response [65] | 7.07E-08 | Plate |
50 | AT1G60190: Armadillo/beta-catenin repeat family/U-box domain-containing | 1.92E-06 | Soil | |
53 | AT5G24120: SIGE/SIG5 (RNA polymerase sigma subunit E); DNA binding/DNA-directed RNA polymerase/sigma/transcription factor | Regulated in blue light by cryptochromes and involved in light-dependent regulation of the photosynthetic apparatus [66]. In a separate study shown to be essential for Arabidopsis[67] | 3.24E-06 | Soil |
55 | AT1G10370: ATGSTU17/ERD9/(Early-Responsive to Dehydration 9) | Dehydration responsive [68] | 4.43E-06 | Plate |
57 | AT1G32900: Starch synthase, putative | Identified in a study on light/cold interactions [69]. Upregulated by cold generally, but upregulated more under cold/light conditions than cold/dark | 6.47E-06 | Novel |
60 | AT4G33905: Peroxisomal membrane protein 22 kDa, putative | Upregulated by stress, including cold treatment [70] | 7.71E-06 | Novel |
61 | AT1G01520: Myb family transcription factor | Upregulated in mutant that has improved freezing tolerance (i.e. esk1 mutant) [71]. | 1.63E-05 | Novel |
63 | AT5G57760: Unknown | 1.95E-05 | Plate | |
70 | AT5G14760: AO (L-aspartate oxidase) | Involved in the synthesis of NAD [72], which is phosphorylated by cold in other plants [73] | 4.96E-05 | Novel |
71 | AT1G10585: Transcription factor | Upregulated under conditions associated with oxidative stress/high light [74] | 5.66E-05 | Soil |
72 | AT5G07010: Sulfotransferase family | Jasmonate responsive [68] | 5.95E-05 | Soil |
75 | AT2G22590: Glycosyltransferase family protein | In the same gene family as UGT91A1, (a target of a TF that regulates flavonol synthesis), and is thus proposed to impact flavonol biosynthesis, which is a product associated with cold response [75, 76] | 6.55E-05 | Plate |
76 | AT3G17609: HYH (HY5-Homolog); DNA binding/transcription factor | Involved in phyB signaling [77]; Required for low temperature-induced anthocyanin accumulation [78] | 6.78E-05 | Novel |
81 | AT1G17170: ATGSTU24 (Arabidopsis thaliana Glutathione S-Transferase (TAU) 24) | Member of the Glutathione S-transferase family (involved in flavonoid synthesis and general abiotic stress response) [79] | 0.000123 | Soil |
82 | AT5G07990: TT7 (Transparent Testa 7); flavonoid 3′-monooxygenase | Flavonoid biosynthesis protein, which is a product associated with cold response [68, 76] | 0.000125 | Plate |
83 | AT3G55940: Phosphoinositide-specific phospholipase C, putative | Phospholipase C genes, to which this is related, have been associated with responses to stress in Arabidopsis[80] | 0.000142 | Plate |
84 | AT3G21560: UGT84A2; UDP-glycosyltransferase/sinapate 1-glucosyltransferase | Upregulated by cold via the phospholipase D-dependent phosphatidic acid production [81] | 0.000145 | Plate |
85 | AT5G49480: ATCP1 (CA2 + −Binding Protein 1) | A “cold regulated signaling gene” that is altered in an ice1 mutant background (ICE1 is a cold/freezing related TF) [51]. Regulation altered under drought conditions [82]. Also (like UGT84A2, above) upregulated by cold via phospholipase D-dependent phosphatidic acid production [81] | 0.000168 | Soil |
86 | AT5G44110: POP1 | Shown to be upregulated by cold in supplemental table of [83]. Response to Red and Far-Red light via phyA [84]. Also a target of HY5[85], which is a transcription factor in light signaling/responsiveness, but also shown to be important for cold dependent anthocyanin accumulation together with HYH (above) [78] | 0.00017 | Soil |
87 | AT5G36910: THI2.2 (Thionin 2.2); toxin receptor binding | Downregulated under high temperature stress [86], associated with jasmonic acid/salicylic acid signalling [87] and target of FAR1 and FHY3, which function in phyA signaling [88] | 0.000174 | Novel |
88 | AT2G31380: STH1 (salt tolerance homologue); transcription factor/zinc ion binding, also previously denoted ZF3 | Like POP1 above, shown to be upregulated by cold in supplemental table of [83]. Circadian-controlled zinc finger gene with role in light signaling [89]. Additional evidence for role in light signaling and regulation by phytochrome [90, 91], and like THI2 (above), target of FAR1 and FHY3, which function in phyA signaling [88] | 0.000176 | Soil |