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

Khadka, Vedbar Singh; Vaughn, Kimberley; Xie, Juan; Swaminathan, Padmapriya; Ma, Qin; Cramer, Grant R.; Fennell, Anne Y.

doi:10.1186/s12870-019-1664-7

BMC Plant Biology

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
Category	VitisNet pathway	Pathway size	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
1.3 Lipid Metabolism	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
1.6 Other Amino Acid Metabolism	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
1.8 Cofactors & Vitamin Metabolism	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
3.3 Plant-specific Signaling	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
4.1 Transport and Catabolism	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
4.3 Cell Growth and Death	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

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

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