Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.4.19.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.32938	0.681
27DAP/17DAP	0.77998	0.304
39DAP/27DAP	1.39196	0.215
41DAP/39DAP	0.88016	0.516
42DAP/41DAP	1.10178	0.908
43DAP/42DAP	0.89002	0.639
47DAP/43DAP	1.12874	0.769
52DAP/47DAP	1.29717	0.485
57DAP/52DAP	1.54659	0.735

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.50314	0.121
17DAP/reference	1.05874	0.427
27DAP/reference	1.09173	0.426
39DAP/reference	0.99924	1
41DAP/reference	1.18855	0.265
42DAP/reference	1.38129	0.021
43DAP/reference	1.04253	0.866
47DAP/reference	1.14354	0.093
52DAP/reference	1.10142	0.663
57DAP/reference	1.16175	0.582

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85873	0.251
27DAP/17DAP	0.87075	0.132
39DAP/27DAP	0.94055	0.502
41DAP/39DAP	1.1098	0.65
42DAP/41DAP	0.99815	0.887
43DAP/42DAP	0.84924	0.024
47DAP/43DAP	1.07536	0.817
52DAP/47DAP	1.18985	0.455
57DAP/52DAP	1.33146	0.115
57DAP/7DAP	1.03899	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84266	0.082
17DAP/reference	0.90599	0.108
27DAP/reference	0.99442	0.656
39DAP/reference	0.94813	0.354
41DAP/reference	1.06419	1
42DAP/reference	1.12723	0.308
43DAP/reference	1.02303	0.764
47DAP/reference	0.88566	0.383
52DAP/reference	0.98149	0.571
57DAP/reference	0.93821	0.26

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00511	0.97
17DAP/reference	1.09337	0.484
27DAP/reference	0.75382	0.067
39DAP/reference	1.0049	0.722
41DAP/reference	0.98927	0.601
42DAP/reference	1.13921	0.259
43DAP/reference	1.13742	0.997
47DAP/reference	1.50162	0.008
52DAP/reference	1.11444	0.181
57DAP/reference	1.16684	0.2

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00582	0.75
17DAP/reference	1.09482	0.578
27DAP/reference	0.85835	0.14
39DAP/reference	1.03939	0.613
41DAP/reference	0.82518	0.107
42DAP/reference	0.85887	0.172
43DAP/reference	1.06102	0.867
47DAP/reference	1.03976	0.901
52DAP/reference	1.00709	1
57DAP/reference	0.81137	0.082

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.80802	1
26DAP/20DAP	1.18233	0.504
34DAP/26DAP	1.16317	0.819
51DAP/34DAP	0.93181	0.624
52DAP/51DAP	1.49453	0.035
53DAP/52DAP	0.81266	0.1
55DAP/53DAP	1.25529	0.058
57DAP/55DAP	0.78271	0.21
62DAP/57DAP	1.04818	1
68DAP/62DAP	1.67348	0.707
68DAP/14DAP	0.83745	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.75583	0.027

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.8353	0.317
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.65046
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	0.81201
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.64804
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.77298
IL12-4/WTpooled	1.55915	0.522
IL1-4/WTpooled	1.18057	1
WT/WTpooled	1.07114

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	1.03494	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08223	0.656
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.08686	1
DC3000/delta hrp 24h	0.81754	0.145

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.1346	0.063
DC3000 delta B/DC3000 delta AB	1.12283	0.403

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	N/A	N/A
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02273	1
Var 0h	1.32974	0.311
Var 12h I row2-row1	0.93917	0.705
Var 12h NI row2-row1	1.13761	1
Var 36h I row2-row1	0.96444	1
Var 36h NI row2-row1	0.90859	0.706
Var 60h I row2-row1	0.8315	0.439
Var 60h NI row2-row1	0.85159	0.483
Time course 0hI-0hNI	0.8563	0.118
Time course 12hI-12hNI	1.03026	0.746
Time course 36hI-36hNI	1.13632	0.355
Time course 60hI-60hNI	1.05441	0.495

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)	N/A	N/A
transgenic ySAMdc/azygous control (breaker)	N/A	N/A
transgenic ySAMdc/azygous control (red)	0.96732	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91654	0.248

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.31468	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	1.56395	0.123
Manapal/WT (red)	N/A	N/A