Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.6.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01401	0.728
27DAP/17DAP	1.02267	0.934
39DAP/27DAP	1.09321	1
41DAP/39DAP	1.4971	0.488
42DAP/41DAP	2.80289	0.021
43DAP/42DAP	1.62181	0.499
47DAP/43DAP	1.22846	0.733
52DAP/47DAP	0.63074	0.165
57DAP/52DAP	1.94943	0.784

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.63648	0.03
17DAP/reference	0.89303	0.278
27DAP/reference	0.79876	0.092
39DAP/reference	1.0145	0.957
41DAP/reference	1.0353	0.808
42DAP/reference	1.23195	0.017
43DAP/reference	1.36051	0.061
47DAP/reference	1.37948	0.007
52DAP/reference	1.24198	0.205
57DAP/reference	0.92954	0.308

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.00272	0.826
27DAP/17DAP	1.08999	0.811
39DAP/27DAP	1.59347	0.626
41DAP/39DAP	0.97148	0.98
42DAP/41DAP	0.98762	0.776
43DAP/42DAP	1.23859	0.015
47DAP/43DAP	0.98859	0.923
52DAP/47DAP	0.97755	0.919
57DAP/52DAP	0.98135	0.804
57DAP/7DAP	0.6818	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93586	0.445
17DAP/reference	0.63436	0.02
27DAP/reference	0.73372	0.045
39DAP/reference	1.03035	0.745
41DAP/reference	1.0132	0.778
42DAP/reference	0.81234	0.275
43DAP/reference	0.97939	0.58
47DAP/reference	0.8777	0.222
52DAP/reference	1.37608	0.025
57DAP/reference	1.12707	0.25

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.65568	0.018
17DAP/reference	0.67183	0.003
27DAP/reference	0.86032	0.097
39DAP/reference	0.81827	0.072
41DAP/reference	0.80537	0.1
42DAP/reference	0.79389	0.05
43DAP/reference	0.84709	0.117
47DAP/reference	0.92697	0.102
52DAP/reference	0.83951	0.025
57DAP/reference	0.84946	0.046

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91447	0.311
17DAP/reference	0.86511	0.281
27DAP/reference	1.41014	0.357
39DAP/reference	0.61866	0.019
41DAP/reference	1.58405	0.129
42DAP/reference	1.14502	0.5
43DAP/reference	1.26417	0.314
47DAP/reference	2.07036	0.005
52DAP/reference	1.81696	0.074
57DAP/reference	0.95526	0.416

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.0767	1
26DAP/20DAP	1.33493	0.385
34DAP/26DAP	0.74006	0.247
51DAP/34DAP	1.06586	0.936
52DAP/51DAP	0.9875	1
53DAP/52DAP	1.09933	0.678
55DAP/53DAP	0.87808	0.725
57DAP/55DAP	0.97331	0.902
62DAP/57DAP	1.35647	0.445
68DAP/62DAP	0.59941	0.579
68DAP/14DAP	1.44181	0.146

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.02299	0.774

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.2607	0.017
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.20673	0.293
Mature Eggplant/Ripe Tomato	0.54736	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.25443	0.742
1-1-2/M82	1.55374	1
12-2/M82	N/A	N/A
12-4/M82	0.88229	1
1-3/M82	1.09245
2-1-1/M82	1.19681	0.764
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.82246
4-3-2/M82	1.92505	0.284
4-3/M82	1.20639
5-3/M82	0.93657	0.49
6-2/M82	N/A	N/A
6-3/M82	0.86201	1
7-1/M82	0.95441
7-2/M82	0.95841
9-3-2/M82	1.54936	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.08629	1
IL2-6/WTpooled	1.16523	0.659
IL7-5/WTpooled	1.25533
IL7-3/WTpooled	1.22372	1
IL12-4/WTpooled	1.01238	1
IL1-4/WTpooled	1.01534
WT/WTpooled	0.98955	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	0.85216	0.975

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.30686	0.894
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	0.89426	1
DC3000/delta hrp 24h	1.32107	0.516

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	0.88322

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	0.96465	1
Var 0h	0.48229	0.457
Var 12h I row2-row1	0.91527	0.39
Var 12h NI row2-row1	1.1635	0.34
Var 36h I row2-row1	1.1481	0.339
Var 36h NI row2-row1	1.07454	1
Var 60h I row2-row1	0.76155	0.374
Var 60h NI row2-row1	0.99548	1
Time course 0hI-0hNI	0.95142	0.734
Time course 12hI-12hNI	1.01867	0.82
Time course 36hI-36hNI	1.08916	0.114
Time course 60hI-60hNI	1.16148	0.096

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	0.82315	0.454
transgenic ySAMdc/azygous control (breaker)	0.85815	0.49
transgenic ySAMdc/azygous control (red)	0.90715	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.16089	0.035

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97004	0.59

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95553	1
Manapal/WT (break)	0.96186	1
Manapal/WT (red)	0.65556	0.242