Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.16.8

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.11271	0.827
27DAP/17DAP	0.51299	0.036
39DAP/27DAP	0.64983	0.326
41DAP/39DAP	0.68367	0.113
42DAP/41DAP	0.82024	0.774
43DAP/42DAP	1.01287	1
47DAP/43DAP	0.72516	0.236
52DAP/47DAP	0.96775	0.898
57DAP/52DAP	1.06395	0.966

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.69714	0.051
17DAP/reference	0.48067	0.008
27DAP/reference	0.5344	0.018
39DAP/reference	0.40283	0.013
41DAP/reference	0.33116	0.009
42DAP/reference	0.45331	0.001
43DAP/reference	0.45995	0.023
47DAP/reference	0.47232	0.003
52DAP/reference	0.43096	0.024
57DAP/reference	0.69825	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.8028	0.036
27DAP/17DAP	0.70986	0.227
39DAP/27DAP	0.38884	0.029
41DAP/39DAP	1.52411	0.061
42DAP/41DAP	0.7623	0.017
43DAP/42DAP	0.62787	0.029
47DAP/43DAP	0.82719	0.125
52DAP/47DAP	0.92778	0.848
57DAP/52DAP	0.93291	0.608
57DAP/7DAP	0.34137	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03826	0.945
17DAP/reference	0.69911	0.013
27DAP/reference	0.52153	0.01
39DAP/reference	0.42756	0.011
41DAP/reference	0.33454	0.009
42DAP/reference	0.30699	0.01
43DAP/reference	0.28634	0.008
47DAP/reference	0.29971	0.03
52DAP/reference	0.32929	0.01
57DAP/reference	0.3564	0.006

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.41536	0.007
17DAP/reference	0.50822	0.011
27DAP/reference	0.556	0.023
39DAP/reference	0.41306	0.011
41DAP/reference	0.47508	0.006
42DAP/reference	0.39313	0.01
43DAP/reference	0.18455	0.002
47DAP/reference	0.28586	0.007
52DAP/reference	0.26253	0.003
57DAP/reference	0.1498	0.002

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.77182	0.019
17DAP/reference	1.67354	0.11
27DAP/reference	1.16072	0.207
39DAP/reference	0.868	0.147
41DAP/reference	0.62812	0.018
42DAP/reference	0.49984	0.019
43DAP/reference	0.4474	0.017
47DAP/reference	0.28285	0.004
52DAP/reference	0.3124	0.047
57DAP/reference	1.1725	0.694

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90311	1
26DAP/20DAP	1.13656	0.793
34DAP/26DAP	0.863	0.519
51DAP/34DAP	0.39612	0.049
52DAP/51DAP	1.00142	1
53DAP/52DAP	0.70273	0.179
55DAP/53DAP	0.85647	0.577
57DAP/55DAP	0.80783	0.173
62DAP/57DAP	1.63908	0.35
68DAP/62DAP	1.32688	0.866
68DAP/14DAP	0.60304	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.55361	0.033

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.21208	0.058
Mature Green Tomato/Ripe Tomato	4.20219	0.026
Immature Eggplant/Mature Eggplant	0.39439	0.062
Ripe Pepper/Ripe Tomato	2.08093	0.258
Mature Eggplant/Ripe Tomato	6.84921	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94864	0.944
1-1-2/M82	1.04035	1
12-2/M82	0.50822	0.535
12-4/M82	0.73628
1-3/M82	1.3558
2-1-1/M82	1.50592	0.229
2-1/M82	0.98437	1
2-6/M82	1.39612
3-2/M82	1.22679
4-1-1/M82	1.59996	0.968
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	1.27611	1
5-3/M82	1.7346	0.572
6-2/M82	N/A	N/A
6-3/M82	0.96426	0.857
7-1/M82	1.09533
7-2/M82	1.42666
9-3-2/M82	1.37378

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.40292	0.456
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.12332	0.362
IL12-4/WTpooled	1.02256	0.785
IL1-4/WTpooled	1.05792
WT/WTpooled	1.0419	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	1.02851	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91075	1
DC3000/delta hrp 6h	1.19221	1
DC3000/delta hrp 12h	0.98813	1
DC3000/delta hrp 24h	N/A	N/A

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.75132	0.081
DC3000 delta B/DC3000 delta AB	0.41618	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.97107	1
Exp 36h	0.84766	0.504
Exp 60h	0.79322	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98181	1
Var 0h	1.19827	0.594
Var 12h I row2-row1	0.90052	0.338
Var 12h NI row2-row1	0.973	0.82
Var 36h I row2-row1	0.88718	0.438
Var 36h NI row2-row1	0.99877	1
Var 60h I row2-row1	1.68606	0.562
Var 60h NI row2-row1	1.12009	0.904
Time course 0hI-0hNI	1.0328	0.603
Time course 12hI-12hNI	1.06397	0.55
Time course 36hI-36hNI	0.90609	0.114
Time course 60hI-60hNI	0.13828	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)	1.09828	0.571
transgenic ySAMdc/azygous control (breaker)	1.99838	0.161
transgenic ySAMdc/azygous control (red)	1.09874	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.50038	0.078

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.68913	0.222

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	6.64424	0.084
Manapal/WT (break)	3.28585	0.123
Manapal/WT (red)	1.16627	1