Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.3.8.14

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.66162	0.073
27DAP/17DAP	0.85155	0.597
39DAP/27DAP	1.91855	0.034
41DAP/39DAP	0.86684	0.473
42DAP/41DAP	2.12555	0.098
43DAP/42DAP	1.5379	0.848
47DAP/43DAP	0.84487	0.504
52DAP/47DAP	0.54524	0.048
57DAP/52DAP	1.10137	0.98

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16245	0.35
17DAP/reference	1.00149	1
27DAP/reference	1.32911	0.01
39DAP/reference	1.10585	0.229
41DAP/reference	1.14714	0.221
42DAP/reference	1.3911	0.001
43DAP/reference	1.218	0.152
47DAP/reference	1.37656	0.001
52DAP/reference	1.5221	0.032
57DAP/reference	1.39541	0.043

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03232	0.934
27DAP/17DAP	0.89319	0.614
39DAP/27DAP	1.1657	0.182
41DAP/39DAP	0.91602	0.747
42DAP/41DAP	1.31929	0.065
43DAP/42DAP	1.93061	0.014
47DAP/43DAP	1.00847	1
52DAP/47DAP	1.1942	0.8
57DAP/52DAP	0.80743	0.219
57DAP/7DAP	1.56548	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18524	0.201
17DAP/reference	1.41171	0.006
27DAP/reference	1.41456	0.008
39DAP/reference	1.45817	0.006
41DAP/reference	1.36086	0.015
42DAP/reference	1.32177	0.008
43DAP/reference	1.41746	0.014
47DAP/reference	1.4926	0.034
52DAP/reference	1.60932	0.008
57DAP/reference	1.51874	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04375	0.993
17DAP/reference	1.48819	0.023
27DAP/reference	1.59469	0.025
39DAP/reference	1.3686	0.013
41DAP/reference	1.90266	0.009
42DAP/reference	1.76383	0.007
43DAP/reference	1.21193	0.704
47DAP/reference	1.34635	0.01
52DAP/reference	1.46764	0.007
57DAP/reference	1.17702	0.374

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.47443	0.017
17DAP/reference	1.22223	0.321
27DAP/reference	1.15608	0.105
39DAP/reference	1.2614	0.007
41DAP/reference	1.43459	0.023
42DAP/reference	1.92029	0.008
43DAP/reference	2.28323	0.007
47DAP/reference	1.80073	0.032
52DAP/reference	1.57939	0.042
57DAP/reference	1.74689	0.007

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.29435	0.878
26DAP/20DAP	1.05104	1
34DAP/26DAP	1.14045	1
51DAP/34DAP	0.54448	0.06
52DAP/51DAP	0.79001	1
53DAP/52DAP	1.01797	0.961
55DAP/53DAP	0.9547	0.698
57DAP/55DAP	0.89937	0.577
62DAP/57DAP	1.14957	0.767
68DAP/62DAP	1.16667	0.95
68DAP/14DAP	1.01428	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.6514	0.055

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.58396	0.063
Mature Green Tomato/Ripe Tomato	1.15252	0.948
Immature Eggplant/Mature Eggplant	0.70977	0.144
Ripe Pepper/Ripe Tomato	1.50452	1
Mature Eggplant/Ripe Tomato	1.23564	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.91422	0.944
1-1-2/M82	1.14247	1
12-2/M82	1.06968	1
12-4/M82	1.5022	1
1-3/M82	1.47164	0.479
2-1-1/M82	1.04302	0.764
2-1/M82	0.71723	0.519
2-6/M82	0.99687	1
3-2/M82	0.81512	1
4-1-1/M82	1.05174	1
4-1/M82	3.85694
4-3-2/M82	1.24173	0.262
4-3/M82	1.06483	1
5-3/M82	1.22377	1
6-2/M82	0.99247	1
6-3/M82	0.94017	1
7-1/M82	0.92233	0.803
7-2/M82	1.06897	1
9-3-2/M82	1.39553	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.05568	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.83393	0.418
IL12-4/WTpooled	0.88663	0.566
IL1-4/WTpooled	0.93924	0.476
WT/WTpooled	0.81934	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	0.95447	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.91494	1
DC3000/delta hrp 6h	1.04354	1
DC3000/delta hrp 12h	0.91058	1
DC3000/delta hrp 24h	0.98154	0.924

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.85608	0.105
DC3000 delta B/DC3000 delta AB	0.842	0.183

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.96804	1
Exp 36h	0.8801	0.749
Exp 60h	0.80392	0.522

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99975	1
Var 0h	1.05169	1
Var 12h I row2-row1	0.83725	0.357
Var 12h NI row2-row1	1.04003	1
Var 36h I row2-row1	1.08591	0.908
Var 36h NI row2-row1	1.00227	0.852
Var 60h I row2-row1	1.05287	1
Var 60h NI row2-row1	0.85707	0.756
Time course 0hI-0hNI	0.9058	0.252
Time course 12hI-12hNI	0.99999	1
Time course 36hI-36hNI	1.12318	0.248
Time course 60hI-60hNI	0.74782	0.015

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)	0.93552	0.454
transgenic ySAMdc/azygous control (breaker)	1.1883	0.248
transgenic ySAMdc/azygous control (red)	0.93052	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89863	0.117

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.50756	0.231

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.32201	0.083
Manapal/WT (break)	1.297	0.381
Manapal/WT (red)	1.05687	1