Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.2.7.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.10354	0.977
27DAP/17DAP	1.73684	0.339
39DAP/27DAP	1.09597	0.833
41DAP/39DAP	1.05541	0.642
42DAP/41DAP	1.07273	0.962
43DAP/42DAP	1.16697	1
47DAP/43DAP	1.19077	0.595
52DAP/47DAP	1.49045	0.449
57DAP/52DAP	1.27055	0.912

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84869	0.052
17DAP/reference	0.95004	0.448
27DAP/reference	1.00222	0.923
39DAP/reference	1.03938	0.557
41DAP/reference	0.97382	0.667
42DAP/reference	0.88148	0.011
43DAP/reference	0.92836	0.377
47DAP/reference	0.93357	0.071
52DAP/reference	0.87161	0.195
57DAP/reference	1.00389	1

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01625	0.763
27DAP/17DAP	1.06623	0.817
39DAP/27DAP	1.30556	0.236
41DAP/39DAP	0.93528	0.793
42DAP/41DAP	0.9886	0.764
43DAP/42DAP	1.53437	0.027
47DAP/43DAP	0.98994	0.954
52DAP/47DAP	1.39816	0.243
57DAP/52DAP	1.44846	0.067
57DAP/7DAP	1.52245	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.82801	0.104
17DAP/reference	0.88026	0.072
27DAP/reference	1.04789	0.804
39DAP/reference	1.0097	1
41DAP/reference	0.97049	0.341
42DAP/reference	1.06747	0.308
43DAP/reference	1.19342	0.074
47DAP/reference	0.95116	0.293
52DAP/reference	1.16143	0.058
57DAP/reference	1.49561	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.92429	0.286
17DAP/reference	0.92484	0.269
27DAP/reference	0.88131	0.188
39DAP/reference	0.96432	0.404
41DAP/reference	0.83541	0.049
42DAP/reference	0.96663	0.321
43DAP/reference	1.0943	0.977
47DAP/reference	1.00601	1
52DAP/reference	0.98956	0.619
57DAP/reference	1.00667	1

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.77298	0.05
17DAP/reference	0.92334	0.433
27DAP/reference	1.06083	0.575
39DAP/reference	1.02393	0.733
41DAP/reference	1.02081	1
42DAP/reference	0.99468	0.816
43DAP/reference	0.85633	0.092
47DAP/reference	0.93399	0.174
52DAP/reference	0.99162	0.838
57DAP/reference	0.77256	0.03

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.9887	1
26DAP/20DAP	1.2025	0.785
34DAP/26DAP	0.67346	0.272
51DAP/34DAP	0.91009	0.737
52DAP/51DAP	0.80791	1
53DAP/52DAP	1.3972	0.697
55DAP/53DAP	0.85547	0.462
57DAP/55DAP	0.83141	0.606
62DAP/57DAP	1.39703	0.393
68DAP/62DAP	N/A	N/A
68DAP/14DAP	0.98736

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.08072	0.018

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.11063	0.417
Mature Green Tomato/Ripe Tomato	0.71207	0.066
Immature Eggplant/Mature Eggplant	1.22585	0.165
Ripe Pepper/Ripe Tomato	1.33759	1
Mature Eggplant/Ripe Tomato	0.85521	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.96847	0.944
1-1-2/M82	1.05862	1
12-2/M82	1.00909	1
12-4/M82	0.89506	0.298
1-3/M82	1.13145	0.479
2-1-1/M82	0.929	0.784
2-1/M82	1.09313	1
2-6/M82	1.03036	1
3-2/M82	1.13318	0.549
4-1-1/M82	0.98013	1
4-1/M82	0.78192	1
4-3-2/M82	0.72896	0.458
4-3/M82	0.88885	1
5-3/M82	0.98273	1
6-2/M82	1.20112
6-3/M82	0.9589	1
7-1/M82	1.09606	1
7-2/M82	0.81809	0.57
9-3-2/M82	0.87294	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.89557	0.321
IL2-6/WTpooled	1.17728	0.788
IL7-5/WTpooled	0.74279	1
IL7-3/WTpooled	1.123	1
IL12-4/WTpooled	0.96412	0.543
IL1-4/WTpooled	0.92344	0.834
WT/WTpooled	0.78295	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	0.93318	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02907	0.774
DC3000/delta hrp 6h	1.32351	1
DC3000/delta hrp 12h	1.03441	1
DC3000/delta hrp 24h	1.18772	0.467

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.44667
DC3000 delta B/DC3000 delta AB	1.69916	0.089

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96037	1
Exp 36h	1.09906	0.693
Exp 60h	1.1952	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01003	1
Var 0h	1.12647	0.98
Var 12h I row2-row1	0.86835	0.514
Var 12h NI row2-row1	0.77074	0.82
Var 36h I row2-row1	1.12934	0.742
Var 36h NI row2-row1	0.9524	0.584
Var 60h I row2-row1	0.84987	0.582
Var 60h NI row2-row1	0.81506	0.69
Time course 0hI-0hNI	1.09609	0.63
Time course 12hI-12hNI	1.06935	0.687
Time course 36hI-36hNI	1.30048	0.007
Time course 60hI-60hNI	1.79185	0.008

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)	1.07664	0.256
transgenic ySAMdc/azygous control (breaker)	1.20381	0.248
transgenic ySAMdc/azygous control (red)	1.17009	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.00446	0.766

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87609	0.284

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.71925	1
Manapal/WT (break)	0.90153	1
Manapal/WT (red)	0.85218	0.315