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Table 3 The top 25 ranked non-COS genes based on treatment-frequency fold change values at 26 hours

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
  1. *“ Cold Upregulation Category” indicates whether a gene was upregulated in the cold when plants were grown in soil (“Soil”), on agar plates (“Plate”), on both growth mediums (“COS”), or on neither (“Novel”) in Vogel et al’s study [54].