Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.3.20.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.47248	0.124
27DAP/17DAP	1.21354	0.804
39DAP/27DAP	1.35585	1
41DAP/39DAP	1.26187	0.437
42DAP/41DAP	1.21626	0.938
43DAP/42DAP	1.59759	0.736
47DAP/43DAP	1.07668	0.943
52DAP/47DAP	1.04543	0.938
57DAP/52DAP	1.0397	0.992

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.63412
17DAP/reference	0.66368
27DAP/reference	0.37013
39DAP/reference	0.69769	0.487
41DAP/reference	0.67869
42DAP/reference	0.77588	0.035
43DAP/reference	0.33158	0.014
47DAP/reference	0.72843	0.003
52DAP/reference	N/A	N/A
57DAP/reference	0.73627	0.009

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36233	0.65
27DAP/17DAP	1.02712	0.969
39DAP/27DAP	1.29164	0.514
41DAP/39DAP	0.82665	0.372
42DAP/41DAP	1.2434	0.446
43DAP/42DAP	1.5253	0.413
47DAP/43DAP	1.36503	0.788
52DAP/47DAP	0.8092	0.433
57DAP/52DAP	1.15616	0.718
57DAP/7DAP	0.70527	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75379	0.091
17DAP/reference	0.88735	0.167
27DAP/reference	0.84798	0.019
39DAP/reference	0.47427	0.014
41DAP/reference	0.4525	0.012
42DAP/reference	0.46675	0.01
43DAP/reference	0.68772	0.014
47DAP/reference	0.84055	0.383
52DAP/reference	0.8957	0.232
57DAP/reference	0.81286	0.093

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81311	0.1
17DAP/reference	0.62968	0.004
27DAP/reference	0.76769	0.111
39DAP/reference	0.66932	0.04
41DAP/reference	0.72303	0.057
42DAP/reference	1.12361	0.81
43DAP/reference	0.83171	0.132
47DAP/reference	0.72543	0.027
52DAP/reference	0.81009	0.043
57DAP/reference	0.71862	0.009

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91571	0.183
17DAP/reference	0.83838	0.092
27DAP/reference	1.01878	0.934
39DAP/reference	0.78015	0.05
41DAP/reference	0.91291	0.064
42DAP/reference	0.92018	0.361
43DAP/reference	1.03411	0.949
47DAP/reference	0.78411	0.017
52DAP/reference	0.89044	0.303
57DAP/reference	0.94168	0.304

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.22769	0.966
26DAP/20DAP	2.46063	0.243
34DAP/26DAP	1.31405
51DAP/34DAP	1.44282	0.84
52DAP/51DAP	2.32373	0.032
53DAP/52DAP	0.56549
55DAP/53DAP	1.3955	0.781
57DAP/55DAP	0.5116	0.046
62DAP/57DAP	1.35913	0.622
68DAP/62DAP	2.99197	0.021
68DAP/14DAP	2.08788	0.029

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.20124	0.814

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.84638	0.226
Immature Eggplant/Mature Eggplant	1.70741
Ripe Pepper/Ripe Tomato	0.55798	0.224
Mature Eggplant/Ripe Tomato	0.81928	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.6968	0.804
12-2/M82	N/A	N/A
12-4/M82	1.91509	1
1-3/M82	1.94733	1
2-1-1/M82	2.07546
2-1/M82	N/A	N/A
2-6/M82	2.32177
3-2/M82	0.7238
4-1-1/M82	N/A	N/A
4-1/M82	0.78255
4-3-2/M82	0.86185	1
4-3/M82	N/A	N/A
5-3/M82	1.6321	1
6-2/M82	3.52499	1
6-3/M82	1.38185	1
7-1/M82	N/A	N/A
7-2/M82	0.40414
9-3-2/M82	0.67437	0.449

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.88067	0.383
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.97703	1
IL12-4/WTpooled	1.18791	0.538
IL1-4/WTpooled	1.04722	1
WT/WTpooled	1.00949	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	1.10554	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.31087	1
DC3000/delta hrp 6h	0.5277	0.95
DC3000/delta hrp 12h	1.02	1
DC3000/delta hrp 24h	0.9848	0.395

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	0.7033

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.93115	1
Exp 36h	0.85134	0.699
Exp 60h	1.04085	0.994

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05896	1
Var 0h	N/A	N/A
Var 12h I row2-row1	1.08351	0.224
Var 12h NI row2-row1	0.86902
Var 36h I row2-row1	1.16385	1
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	0.64847	1
Time course 0hI-0hNI	1.05094	0.867
Time course 12hI-12hNI	1.14958	0.824
Time course 36hI-36hNI	1.03975	0.975
Time course 60hI-60hNI	1.07298	0.216

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)	0.87315	0.409
transgenic ySAMdc/azygous control (breaker)	0.85834	0.251
transgenic ySAMdc/azygous control (red)	0.98373	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.01768	0.525

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.65264	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.98898	1
Manapal/WT (break)	0.74361	0.333
Manapal/WT (red)	0.75575	0.216