Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.1.13.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9775	0.811
27DAP/17DAP	1.00915	1
39DAP/27DAP	1.0207	0.876
41DAP/39DAP	1.12806	0.797
42DAP/41DAP	1.25785	0.863
43DAP/42DAP	1.1402	0.918
47DAP/43DAP	0.84881	0.533
52DAP/47DAP	0.89686	0.668
57DAP/52DAP	1.32303	0.764

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89752	0.154
17DAP/reference	0.89209	0.022
27DAP/reference	1.04853	0.672
39DAP/reference	0.96993	0.611
41DAP/reference	0.90822	0.154
42DAP/reference	0.90934	0.014
43DAP/reference	1.04979	0.596
47DAP/reference	1.11061	0.114
52DAP/reference	0.96568	0.416
57DAP/reference	1.04655	0.662

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.28258	0.129
27DAP/17DAP	1.11797	0.383
39DAP/27DAP	1.17741	0.236
41DAP/39DAP	0.98736	1
42DAP/41DAP	1.14913	0.46
43DAP/42DAP	0.81094	0.111
47DAP/43DAP	1.13726	0.572
52DAP/47DAP	0.92101	0.719
57DAP/52DAP	0.66425	0.141
57DAP/7DAP	0.7289	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.47509	0.046
17DAP/reference	0.95524	0.389
27DAP/reference	0.97466	0.375
39DAP/reference	1.09869	0.267
41DAP/reference	0.9483	0.284
42DAP/reference	0.92709	0.073
43DAP/reference	0.96724	0.368
47DAP/reference	1.0521	0.837
52DAP/reference	0.99159	0.621
57DAP/reference	1.05206	0.698

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84615	0.129
17DAP/reference	0.71693	0.006
27DAP/reference	0.79463	0.033
39DAP/reference	0.80862	0.014
41DAP/reference	0.86275	0.103
42DAP/reference	0.78515	0.013
43DAP/reference	0.86574	0.147
47DAP/reference	0.91163	0.079
52DAP/reference	0.85179	0.04
57DAP/reference	0.75518	0.046

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.29746	0.06
17DAP/reference	0.86504	0.159
27DAP/reference	1.11438	0.137
39DAP/reference	1.11623	0.108
41DAP/reference	0.9682	0.512
42DAP/reference	0.94856	0.445
43DAP/reference	0.99564	0.685
47DAP/reference	0.90538	0.015
52DAP/reference	1.31176	0.148
57DAP/reference	1.00472	0.779

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.85424	0.65
26DAP/20DAP	3.68501	0.128
34DAP/26DAP	0.7631	0.448
51DAP/34DAP	3.34682	0.03
52DAP/51DAP	1.10776	0.565
53DAP/52DAP	0.98312	0.902
55DAP/53DAP	0.49828	0.018
57DAP/55DAP	1.24135	0.185
62DAP/57DAP	1.0766	0.868
68DAP/62DAP	2.05664	0.124
68DAP/14DAP	2.90482	0.021

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.36928	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.81406	0.268
Mature Green Tomato/Ripe Tomato	1.08177	0.881
Immature Eggplant/Mature Eggplant	1.51485	0.07
Ripe Pepper/Ripe Tomato	2.4259	0.258
Mature Eggplant/Ripe Tomato	1.33643	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12022	0.591
1-1-2/M82	1.40815	1
12-2/M82	0.93068	0.955
12-4/M82	1.33244	1
1-3/M82	1.39516	1
2-1-1/M82	1.06967
2-1/M82	0.85383	0.322
2-6/M82	1.22281	0.425
3-2/M82	0.47983
4-1-1/M82	0.9456	1
4-1/M82	2.17983	1
4-3-2/M82	1.44901	0.508
4-3/M82	2.38908	0.268
5-3/M82	1.06958	1
6-2/M82	1.26629
6-3/M82	0.99435	1
7-1/M82	0.66704	0.509
7-2/M82	0.98029	0.796
9-3-2/M82	1.78908

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.11504	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.78191	0.31
IL12-4/WTpooled	0.96112	0.71
IL1-4/WTpooled	0.94939	1
WT/WTpooled	0.92507	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	1.09717	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.04135	0.921
DC3000/delta hrp 6h	1.05495	1
DC3000/delta hrp 12h	1.01049	1
DC3000/delta hrp 24h	1.32775	0.051

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.38449	0.055
DC3000 delta B/DC3000 delta AB	1.36638	0.117

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.5802	1
Exp 36h	1.1214	1
Exp 60h	1.18289	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0007	1
Var 0h	0.63571	1
Var 12h I row2-row1	1.14149	0.506
Var 12h NI row2-row1	1.19311	0.34
Var 36h I row2-row1	1.00491	1
Var 36h NI row2-row1	1.07945	1
Var 60h I row2-row1	0.90232	0.832
Var 60h NI row2-row1	0.90882	0.977
Time course 0hI-0hNI	1.05426	0.764
Time course 12hI-12hNI	1.21188	0.137
Time course 36hI-36hNI	1.28157	0.008
Time course 60hI-60hNI	1.11995	0.302

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)	1.0245	0.482
transgenic ySAMdc/azygous control (breaker)	0.68264	0.15
transgenic ySAMdc/azygous control (red)	0.95143	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94951	0.093

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.14875	0.227

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.0548	1
Manapal/WT (break)	0.79221	1
Manapal/WT (red)	0.79856	0.315