Tomato Functional Genomics Database (TFGD)

Expression of 1-1-8.4.18.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	2.37754	0.037
27DAP/17DAP	0.78669	0.381
39DAP/27DAP	0.91079	0.522
41DAP/39DAP	0.96955	0.862
42DAP/41DAP	0.98011	1
43DAP/42DAP	0.75129	0.456
47DAP/43DAP	2.24704	0.215
52DAP/47DAP	0.86817	0.637
57DAP/52DAP	1.14577	0.859

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02532	1
17DAP/reference	1.31817	0.185
27DAP/reference	1.39855	0.061
39DAP/reference	1.18637	0.311
41DAP/reference	1.22932	0.187
42DAP/reference	0.82387	0.005
43DAP/reference	0.9422	0.316
47DAP/reference	1.17435	0.065
52DAP/reference	1.27349	0.102
57DAP/reference	1.29335	0.034

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83486	0.185
27DAP/17DAP	1.10785	0.587
39DAP/27DAP	1.06599	0.832
41DAP/39DAP	0.93138	0.839
42DAP/41DAP	0.98134	0.781
43DAP/42DAP	0.73024	0.022
47DAP/43DAP	0.80325	0.064
52DAP/47DAP	1.09959	0.689
57DAP/52DAP	0.70639	0.119
57DAP/7DAP	0.56368	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12616	0.613
17DAP/reference	1.07132	0.244
27DAP/reference	1.22053	0.014
39DAP/reference	1.45591	0.027
41DAP/reference	1.01894	1
42DAP/reference	1.02041	0.686
43DAP/reference	1.12435	0.408
47DAP/reference	1.12312	0.537
52DAP/reference	1.26842	0.048
57DAP/reference	1.28214	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08804	0.776
17DAP/reference	0.93308	0.253
27DAP/reference	0.85852	0.188
39DAP/reference	1.22388	0.043
41DAP/reference	0.76233	0.034
42DAP/reference	0.94221	0.355
43DAP/reference	1.06808	0.899
47DAP/reference	0.88621	0.11
52DAP/reference	0.7676	0.016
57DAP/reference	0.92292	0.259

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06067	0.74
17DAP/reference	1.03075	0.854
27DAP/reference	1.21187	0.048
39DAP/reference	1.054	0.342
41DAP/reference	1.05053	0.605
42DAP/reference	1.07277	0.55
43DAP/reference	0.87342	0.15
47DAP/reference	0.77467	0.008
52DAP/reference	1.19654	0.77
57DAP/reference	1.06229	0.717

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.2055	0.966
26DAP/20DAP	1.49251	0.62
34DAP/26DAP	1.10851	0.954
51DAP/34DAP	0.82195	0.323
52DAP/51DAP	0.86543	1
53DAP/52DAP	1.24367	0.594
55DAP/53DAP	1.11981	1
57DAP/55DAP	0.97964	0.867
62DAP/57DAP	0.90287	0.681
68DAP/62DAP	1.69043	0.316
68DAP/14DAP	0.71491	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.52215	0.028

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.77708
Mature Green Tomato/Ripe Tomato	2.1033	0.015
Immature Eggplant/Mature Eggplant	0.66558	0.366
Ripe Pepper/Ripe Tomato	0.17302	0.224
Mature Eggplant/Ripe Tomato	0.25467	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.87699	0.69
1-1-2/M82	1.10768	1
12-2/M82	0.95782	1
12-4/M82	0.98597	1
1-3/M82	1.17677	1
2-1-1/M82	0.9473	1
2-1/M82	0.86199	0.325
2-6/M82	0.83827	1
3-2/M82	0.60167	0.455
4-1-1/M82	1.15501	1
4-1/M82	1.08156
4-3-2/M82	0.63645	0.445
4-3/M82	0.8564	0.72
5-3/M82	1.00751	1
6-2/M82	0.16309	0.497
6-3/M82	1.17138	1
7-1/M82	1.04938	1
7-2/M82	0.952	1
9-3-2/M82	1.16662	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.79272	0.243
IL2-6/WTpooled	0.9314	1
IL7-5/WTpooled	0.82805	1
IL7-3/WTpooled	0.95811	1
IL12-4/WTpooled	1.11533	0.546
IL1-4/WTpooled	0.99451	1
WT/WTpooled	1.0627	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	0.91206	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.15138	0.692
DC3000/delta hrp 6h	1.04376	1
DC3000/delta hrp 12h	1.13864	1
DC3000/delta hrp 24h	0.67989	0.034

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.7806	0.328
Exp 36h	0.78415	0.699
Exp 60h	0.50072	0.258

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

hybridization	ratio	FDR (corrected p value)
self-self	0.95206	1
Var 0h	1.29008	1
Var 12h I row2-row1	1.25965	0.654
Var 12h NI row2-row1	0.82097	0.627
Var 36h I row2-row1	0.73482	0.313
Var 36h NI row2-row1	1.61851	1
Var 60h I row2-row1	1.05627	1
Var 60h NI row2-row1	2.69851	0.904
Time course 0hI-0hNI	1.02706	1
Time course 12hI-12hNI	0.86223	0.32
Time course 36hI-36hNI	0.74117	0.026
Time course 60hI-60hNI	1.64921	0.161

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)	1.12801	0.455
transgenic ySAMdc/azygous control (breaker)	1.01587	1
transgenic ySAMdc/azygous control (red)	0.69857	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02481	0.556

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.4172	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.86315	1
Manapal/WT (break)	0.84018	1
Manapal/WT (red)	0.56609	0.181