Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.3.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03454	0.975
27DAP/17DAP	0.96585	0.882
39DAP/27DAP	0.89734	0.537
41DAP/39DAP	1.00242	0.962
42DAP/41DAP	0.84011	1
43DAP/42DAP	0.96151	0.895
47DAP/43DAP	1.09099	0.584
52DAP/47DAP	0.9594	0.842
57DAP/52DAP	0.63421	0.666

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.05579	0.685
17DAP/reference	0.97593	0.664
27DAP/reference	0.99392	0.741
39DAP/reference	1.17539	0.191
41DAP/reference	0.9874	1
42DAP/reference	0.94576	0.25
43DAP/reference	0.82642	0.148
47DAP/reference	0.88953	0.161
52DAP/reference	1.00562	1
57DAP/reference	1.06225	0.662

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.84041	0.038
27DAP/17DAP	0.65738	0.137
39DAP/27DAP	0.65073	0.029
41DAP/39DAP	1.33872	0.112
42DAP/41DAP	0.98147	0.777
43DAP/42DAP	0.82776	0.189
47DAP/43DAP	0.89001	0.254
52DAP/47DAP	0.87529	0.452
57DAP/52DAP	1.02165	0.902
57DAP/7DAP	0.84886	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02141	0.927
17DAP/reference	0.92361	0.072
27DAP/reference	0.86836	0.011
39DAP/reference	0.92779	0.012
41DAP/reference	0.82892	0.029
42DAP/reference	0.80105	0.01
43DAP/reference	0.81516	0.017
47DAP/reference	0.92072	0.222
52DAP/reference	0.86599	0.014
57DAP/reference	0.93909	0.25

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13236	0.443
17DAP/reference	0.98306	0.611
27DAP/reference	1.092	0.735
39DAP/reference	1.41065	0.056
41DAP/reference	1.13148	0.416
42DAP/reference	1.12056	0.359
43DAP/reference	0.90392	0.32
47DAP/reference	1.05345	0.816
52DAP/reference	1.18146	0.043
57DAP/reference	0.88062	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.94173	0.135
17DAP/reference	0.87341	0.214
27DAP/reference	0.92872	0.102
39DAP/reference	0.93042	0.063
41DAP/reference	0.92046	0.046
42DAP/reference	0.86844	0.087
43DAP/reference	1.02047	0.858
47DAP/reference	0.9509	0.396
52DAP/reference	0.84853	0.177
57DAP/reference	1.32698	0.144

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.82147	1
26DAP/20DAP	1.39851	0.262
34DAP/26DAP	0.94604	0.874
51DAP/34DAP	1.50644	0.207
52DAP/51DAP	0.86106	0.151
53DAP/52DAP	1.18522	0.261
55DAP/53DAP	0.85806	0.404
57DAP/55DAP	1.3315	0.525
62DAP/57DAP	0.81382	0.005
68DAP/62DAP	0.95251	0.81
68DAP/14DAP	1.86299	0.113

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.45401	0.019

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.58807	0.121
Mature Green Tomato/Ripe Tomato	1.90965	0.03
Immature Eggplant/Mature Eggplant	1.66657	0.05
Ripe Pepper/Ripe Tomato	3.4759	0.256
Mature Eggplant/Ripe Tomato	0.91533	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.32402	0.591
1-1-2/M82	0.98171	1
12-2/M82	N/A	N/A
12-4/M82	0.78375	0.319
1-3/M82	1.1743
2-1-1/M82	0.89101
2-1/M82	0.97537
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	0.85115
4-1/M82	N/A	N/A
4-3-2/M82	0.78286
4-3/M82	0.90491	1
5-3/M82	1.3916	0.572
6-2/M82	0.70371
6-3/M82	1.04132
7-1/M82	N/A	N/A
7-2/M82	0.76099
9-3-2/M82	0.65618	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.91069
IL2-6/WTpooled	0.7081
IL7-5/WTpooled	0.67052
IL7-3/WTpooled	0.69105	0.298
IL12-4/WTpooled	0.7443	0.543
IL1-4/WTpooled	1.16678
WT/WTpooled	1.3815	0.874

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	0.87141	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.84425	0.941
DC3000/delta hrp 6h	0.9507	0.95
DC3000/delta hrp 12h	1.16302	1
DC3000/delta hrp 24h	1.04705	0.69

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.73389	0.071
DC3000 delta B/DC3000 delta AB	0.60851	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.6917	1
Exp 36h	0.79114	0.449
Exp 60h	0.6845	0.257

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99451	1
Var 0h	1.05963	0.936
Var 12h I row2-row1	0.78075	0.338
Var 12h NI row2-row1	1.05223	1
Var 36h I row2-row1	0.96676	1
Var 36h NI row2-row1	1.15034	1
Var 60h I row2-row1	1.12075	1
Var 60h NI row2-row1	0.99188	1
Time course 0hI-0hNI	0.8974	0.306
Time course 12hI-12hNI	1.03138	0.798
Time course 36hI-36hNI	0.83717	0.024
Time course 60hI-60hNI	0.29937	0.005

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)	0.96918	0.662
transgenic ySAMdc/azygous control (breaker)	1.016	1
transgenic ySAMdc/azygous control (red)	1.00523	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.26934	0.041

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.05101	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.22906	0.09
Manapal/WT (break)	1.1421	0.381
Manapal/WT (red)	1.43763	0.15