Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.3.2.16

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04208	0.997
27DAP/17DAP	0.69048	0.083
39DAP/27DAP	0.87763	0.397
41DAP/39DAP	0.83069	0.381
42DAP/41DAP	1.13799	0.974
43DAP/42DAP	1.24536	0.58
47DAP/43DAP	0.99031	0.902
52DAP/47DAP	0.79045	0.499
57DAP/52DAP	0.96327	0.94

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06762	0.611
17DAP/reference	1.21325	0.166
27DAP/reference	1.33623	0.115
39DAP/reference	1.18844	0.286
41DAP/reference	1.19658	0.102
42DAP/reference	1.1971	0.108
43DAP/reference	1.05934	0.838
47DAP/reference	1.17338	0.136
52DAP/reference	1.38283	0.038
57DAP/reference	1.26639	0.122

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9207	0.47
27DAP/17DAP	1.03007	0.924
39DAP/27DAP	0.60837	0.037
41DAP/39DAP	0.81983	0.53
42DAP/41DAP	0.90606	0.466
43DAP/42DAP	0.88742	0.321
47DAP/43DAP	0.99063	0.961
52DAP/47DAP	1.13994	0.669
57DAP/52DAP	0.99384	0.726
57DAP/7DAP	1.04843	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03235	1
17DAP/reference	1.3172	0.07
27DAP/reference	1.23163	0.131
39DAP/reference	1.33488	0.021
41DAP/reference	0.97944	0.512
42DAP/reference	0.9286	0.436
43DAP/reference	0.87927	0.305
47DAP/reference	1.33996	0.353
52DAP/reference	1.05912	1
57DAP/reference	1.05071	0.5

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.48356	0.304
17DAP/reference	1.58289	0.083
27DAP/reference	1.06976	0.735
39DAP/reference	1.09182	0.602
41DAP/reference	1.1252	0.981
42DAP/reference	1.19806	0.024
43DAP/reference	1.01743	0.892
47DAP/reference	1.3829	0.008
52DAP/reference	1.2658	0.046
57DAP/reference	1.5367	0.214

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.65553	0.029
17DAP/reference	1.21974	0.545
27DAP/reference	1.22773	0.34
39DAP/reference	1.48778	0.024
41DAP/reference	1.00012	0.826
42DAP/reference	1.40694	0.029
43DAP/reference	1.11397	0.721
47DAP/reference	1.2444	0.76
52DAP/reference	1.23903	0.601
57DAP/reference	1.21207	0.095

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.90294
26DAP/20DAP	1.08862	0.806
34DAP/26DAP	1.03526	1
51DAP/34DAP	0.89318	0.504
52DAP/51DAP	0.94227	1
53DAP/52DAP	1.0243	0.961
55DAP/53DAP	0.71316	0.06
57DAP/55DAP	0.87976	0.612
62DAP/57DAP	0.82438	0.681
68DAP/62DAP	0.97462	0.914
68DAP/14DAP	1.5773	0.469

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.37722	0.021

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	4.0192	0.015
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
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	N/A	N/A
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	0.75857	0.243
IL2-6/WTpooled	1.03827	1
IL7-5/WTpooled	1.00527	1
IL7-3/WTpooled	0.87394	0.298
IL12-4/WTpooled	0.8935	0.581
IL1-4/WTpooled	0.93518	0.834
WT/WTpooled	0.98132	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	0.99027	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.08254	0.894
DC3000/delta hrp 6h	1.06604	1
DC3000/delta hrp 12h	1.0058	1
DC3000/delta hrp 24h	0.81502	0.202

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.50968	0.027
DC3000 delta B/DC3000 delta AB	0.60606	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.74812	0.328
Exp 36h	0.72681	0.419
Exp 60h	0.76171	0.259

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

hybridization	ratio	FDR (corrected p value)
self-self	1.0395	1
Var 0h	0.94984	1
Var 12h I row2-row1	0.76986	0.357
Var 12h NI row2-row1	0.98626	0.906
Var 36h I row2-row1	1.13049	1
Var 36h NI row2-row1	0.85752	0.743
Var 60h I row2-row1	1.05458	0.562
Var 60h NI row2-row1	1.12284	1
Time course 0hI-0hNI	0.99143	1
Time course 12hI-12hNI	0.97799	0.882
Time course 36hI-36hNI	0.81069	0.062
Time course 60hI-60hNI	0.12009	0.005

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)	1.1898	0.318
transgenic ySAMdc/azygous control (breaker)	1.38236	0.248
transgenic ySAMdc/azygous control (red)	1.3302	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.8793	0.072

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.41754	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.72734	0.083
Manapal/WT (break)	3.39964	0.123
Manapal/WT (red)	N/A	N/A