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Table 2 VitisNet pathway enrichment in water deficit root and shoot

From: Transcriptomic response is more sensitive to water deficit in shoots than roots of Vitis riparia (Michx.)

Category VitisNet pathway Pathway size Root Shoot
NES FDR q-val NES FDR q-val
1.1 Carbohydrate Metabolism VV10052 Galactose Metabolism 149 1.59 0.17 1.54 0.18
VV10520 Nucleotide Sugars Metabolism 61 −1.48 0.30 −1.88 0.01
VV10530 Aminosugars Metabolism 79 1.10 0.90 −1.64 0.09
1.2 Energy Metabolism VV10195 Photosynthesis 114 1.74 0.09 1.13 0.47
VV10196 Photosynthesis Antenna Proteins 19 1.99 0.00 −0.86 1.00
VV10680 Methane Metabolism 113 1.56 0.17 −1.60 0.11
1.3 Lipid Metabolism VV10061 Fatty Acid Biosynthesis 70 −1.83 0.09 −1.64 0.09
VV10561 Glycerolipid Metabolism 144 1.09 0.91 1.55 0.20
1.5 Amino Acid Metabolism VV10360 Tyrosine Metabolism 147 1.12 0.88 −1.46 0.23
VV10400 Phenylalanine Metabolism 200 0.95 0.97 −1.71 0.06
VV10400 Phenylalanine Tyrosine & Tryptophan Biosynthesis 143 1.12 0.88 −1.55 0.16
1.6 Other Amino Acid Metabolism VV10460 Cyanoamino Acid Metabolism 34 1.60 0.16 2.00 0.02
VV10480 Glutathione Metabolism 131 1.26 0.58 2.23 0.00
1.7 Glycan Biosynthesis & Metabolism VV10511N-Glycan Degradation 65 0.85 1.00 −1.67 0.08
1.8 Cofactors & Vitamin Metabolism VV10790 Folate Biosynthesis 30 1.24 0.62 1.56 0.20
VV10860 Porphyrin and Chlorophyll Metabolism 64 1.60 0.17 1.18 0.52
1.9 Biosynthesis of Secondary Metabolites VV10900 Terpenoid Biosynthesis 156 0.93 0.99 −1.53 0.18
VV10902 Monoterpenoid Biosynthesis 181 1.46 0.29 1.61 0.18
VV10904 Diterpenoid Biosynthesis 68 −1.18 0.72 −1.45 0.23
VV10906 Carotenoid Biosynthesis 41 1.29 0.52 2.05 0.02
VV10940 Phenylpropanoid Biosynthesis 222 0.68 1.00 −1.80 0.03
VV11002 Auxin Biosynthesis 90 1.20 0.69 1.58 0.20
VV11013 ABA Biosynthesis 16 1.88 0.02 1.98 0.02
1.10 Other Metabolism VV11000 Single Reactions 167 1.54 0.18 −1.57 0.14
2.4 Replication and Repair VV23030 DNA Replication 64 −1.40 0.36 −1.63 0.09
3.2 Hormone Signaling VV30003 ABA Signaling 151 1.61 0.17 1.15 0.53
VV30007 Auxin Signaling 271 0.98 0.97 −2.03 0.00
VV30007 Cytokinin Signaling 68 1.56 0.19 1.46 0.25
VV30010 Gibberellin Signaling 36 −1.93 0.07 −1.61 0.11
3.3 Plant-specific Signaling VV34627 R Proteins from Plant Pathogen Interaction 349 0.71 1.00 −2.03 0.00
Circadian Rhythm 64 1.58 0.17 1.15 0.52
4.1 Transport and Catabolism VV44140 Regulation of Autophagy 26 1.56 0.16 1.55 0.18
VV44145 Phagosome 118 −1.80 0.09 −1.45 0.23
4.2 Cell Motility VV44180 Regulation of Actin Cytoskeleton 343 −0.96 1.00 −2.07 0.00
4.3 Cell Growth and Death VV40006 Cell Wall 454 1.05 0.94 −1.72 0.07
VV44110 Cell Cycle 323 −0.96 1.00 −2.16 0.00
5.1 Membrane Transport VV52010 ABC Transporters 239 0.98 0.98 1.49 0.22
5.2 Hormone Transport VV50004 Auxin Transport 52 1.13 0.86 −1.69 0.07
5.3 Transport System VV50113 Thylakoid Targeting Pathway 48 1.72 0.07 −1.22 0.49
5.4 Transporter Catalog VV50105 Transport Electron Carriers 61 1.74 0.07 −0.65 1.00
VV50122 Porters Cat 7 to 17 237 1.32 0.51 −1.44 0.23
VV50135 Primary Active Transporter Cat D2 to E2 81 1.16 0.80 1.84 0.04
6.0 Transcription Factors VV60003 AP2 EREBP 137 1.34 0.50 −1.49 0.20
VV60004 ARF 29 0.79 1.00 −1.48 0.21
VV60008 AUXIAA 23 1.00 0.97 −1.68 0.07
VV60011 BHLH 148 1.24 0.61 −1.72 0.07
VV60015 C2C2-DOF 25 1.63 0.16 −1.05 0.74
VV60019 C2C2-YABBY 7 1.72 0.08 −1.27 0.46
VV60022 CPP 7 1.21 0.66 −1.49 0.20
VV60029 G2-LIKE 37 1.54 0.18 1.30 0.37
VV60033 GRF 12 −0.74 1.00 −1.50 0.19
VV60044 MYB 166 0.96 0.97 −1.51 0.19
VV60046 NAC 75 1.65 0.14 1.88 0.04
VV60055 SBP 20 1.26 0.57 −1.51 0.19
VV60061 TCP 19 0.89 1.00 −1.52 0.19
VV60070 ORPHANS CCT 8 −1.77 0.08 −1.44 0.24
VV60073 ORPHANS ZF-B BOX 15 1.27 0.55 1.87 0.041
VV60077 OTHER ZF-AN1 13 1.53 0.19 1.74 0.08
VV60079 OTHER ZF-DHHC 23 −0.91 1.00 −1.48 0.21
VV60082 GNAT 36 1.56 0.18 −0.89 0.99
  1. A positive normalized enrichment score (NES) indicates VitisNet pathways enriched in WD tissues and a negative NES indicates pathways enriched in C treatments at nominal p-value < 0.05 and false discovery rate (FDR) q-value < 25%. Bold indicates an enrichment in both root and shoot