Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.4.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0741	0.739
27DAP/17DAP	1.11579	0.859
39DAP/27DAP	1.04102	1
41DAP/39DAP	1.1831	0.344
42DAP/41DAP	1.24249	0.644
43DAP/42DAP	0.90414	0.705
47DAP/43DAP	1.26684	0.288
52DAP/47DAP	1.04235	0.991
57DAP/52DAP	0.98134	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02663	0.71
17DAP/reference	1.10905	0.045
27DAP/reference	1.04003	0.599
39DAP/reference	0.94309	0.404
41DAP/reference	0.99768	1
42DAP/reference	1.01192	1
43DAP/reference	1.02077	0.787
47DAP/reference	0.99756	0.674
52DAP/reference	1.06485	0.371
57DAP/reference	0.9816	0.553

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02221	0.934
27DAP/17DAP	1.17257	0.353
39DAP/27DAP	0.88533	0.444
41DAP/39DAP	1.2125	0.044
42DAP/41DAP	0.88604	0.245
43DAP/42DAP	0.97446	0.729
47DAP/43DAP	1.06578	0.963
52DAP/47DAP	0.98904	0.93
57DAP/52DAP	0.99848	0.892
57DAP/7DAP	1.27451	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96266	0.224
17DAP/reference	1.07464	0.134
27DAP/reference	1.03303	0.301
39DAP/reference	0.98569	0.198
41DAP/reference	1.00706	1
42DAP/reference	0.99067	0.612
43DAP/reference	0.84229	0.025
47DAP/reference	1.07124	0.582
52DAP/reference	0.84683	0.028
57DAP/reference	0.85707	0.021

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97424	0.623
17DAP/reference	0.91644	0.106
27DAP/reference	0.94678	0.292
39DAP/reference	1.02149	0.912
41DAP/reference	0.97463	0.481
42DAP/reference	0.98037	0.355
43DAP/reference	0.96988	0.569
47DAP/reference	0.96411	0.194
52DAP/reference	1.02924	0.393
57DAP/reference	0.9041	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88981	0.037
17DAP/reference	0.99422	0.81
27DAP/reference	0.85387	0.046
39DAP/reference	0.79979	0.009
41DAP/reference	0.8741	0.043
42DAP/reference	0.95195	0.445
43DAP/reference	0.90442	0.216
47DAP/reference	1.02085	1
52DAP/reference	0.77204	0.109
57DAP/reference	1.11186	0.717

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97216	1
26DAP/20DAP	1.08073	0.762
34DAP/26DAP	0.95217	0.879
51DAP/34DAP	1.00938	0.978
52DAP/51DAP	0.90247	1
53DAP/52DAP	1.22938	0.296
55DAP/53DAP	1.15827	0.236
57DAP/55DAP	1.20978	0.13
62DAP/57DAP	N/A	N/A
68DAP/62DAP	1.09824	0.31
68DAP/14DAP	1.14308	0.403

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.70419	0.048

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.50224	0.101
Mature Green Tomato/Ripe Tomato	1.00947	0.774
Immature Eggplant/Mature Eggplant	0.92418	0.493
Ripe Pepper/Ripe Tomato	6.64797
Mature Eggplant/Ripe Tomato	2.872	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.95875	0.944
1-1-2/M82	0.90088	0.958
12-2/M82	1.11996	1
12-4/M82	1.00073	1
1-3/M82	0.96387	1
2-1-1/M82	1.11521	1
2-1/M82	1.22767	1
2-6/M82	1.17613	0.505
3-2/M82	0.90086	0.455
4-1-1/M82	1.03461	1
4-1/M82	0.94974
4-3-2/M82	1.05183	1
4-3/M82	0.8651	0.72
5-3/M82	1.07085	1
6-2/M82	1.07012	1
6-3/M82	1.00732	1
7-1/M82	1.07756	1
7-2/M82	1.05389	1
9-3-2/M82	0.89734	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.99068	1
IL2-6/WTpooled	0.37379
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.77812
IL12-4/WTpooled	0.50439	0.71
IL1-4/WTpooled	0.92104	0.834
WT/WTpooled	0.87542	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	1.12905	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.0455	0.921
DC3000/delta hrp 6h	0.88484	0.95
DC3000/delta hrp 12h	1.5062
DC3000/delta hrp 24h	1.12704	0.582

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.06944	0.441
DC3000 delta B/DC3000 delta AB	0.89373	0.279

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90214	1
Exp 36h	1.04376	0.409
Exp 60h	0.98892	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01941	1
Var 0h	1.02055	1
Var 12h I row2-row1	0.87131	0.627
Var 12h NI row2-row1	0.83107	0.546
Var 36h I row2-row1	1.22164	0.41
Var 36h NI row2-row1	1.1602	1
Var 60h I row2-row1	1.07716	1
Var 60h NI row2-row1	1.02894	1
Time course 0hI-0hNI	0.98044	0.94
Time course 12hI-12hNI	1.00001	1
Time course 36hI-36hNI	0.9414	0.274
Time course 60hI-60hNI	0.42919	0.006

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)	0.91952	0.348
transgenic ySAMdc/azygous control (breaker)	1.19538	0.178
transgenic ySAMdc/azygous control (red)	1.15377	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99654	0.858

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98872	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.90356	1
Manapal/WT (break)	1.01598	1
Manapal/WT (red)	0.86065	0.36