Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.8.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87904	0.436
27DAP/17DAP	1.15234	0.868
39DAP/27DAP	0.85866	0.512
41DAP/39DAP	1.18012	0.624
42DAP/41DAP	1.09002	0.945
43DAP/42DAP	1.28531	0.655
47DAP/43DAP	0.68887	0.18
52DAP/47DAP	1.04896	0.953
57DAP/52DAP	1.09455	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68833	0.027
17DAP/reference	0.89494	0.208
27DAP/reference	0.88971	0.339
39DAP/reference	0.86919	0.159
41DAP/reference	0.95063	0.434
42DAP/reference	0.90278	0.091
43DAP/reference	1.03142	0.928
47DAP/reference	0.854	0.042
52DAP/reference	0.92565	0.244
57DAP/reference	1.05365	0.28

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.05396	1
27DAP/17DAP	0.89788	0.418
39DAP/27DAP	1.07432	0.643
41DAP/39DAP	1.0055	1
42DAP/41DAP	0.99281	0.84
43DAP/42DAP	1.03404	0.627
47DAP/43DAP	0.98695	0.933
52DAP/47DAP	1.03472	0.856
57DAP/52DAP	0.92528	0.531
57DAP/7DAP	1.10563

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.75558	0.06
17DAP/reference	0.83977	0.013
27DAP/reference	0.87279	0.076
39DAP/reference	0.89712	0.023
41DAP/reference	0.89437	0.139
42DAP/reference	0.96856	0.458
43DAP/reference	0.84258	0.034
47DAP/reference	0.84937	0.101
52DAP/reference	0.68162	0.02
57DAP/reference	0.72108	0.011

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.68442	0.01
17DAP/reference	0.71439	0.015
27DAP/reference	0.74538	0.014
39DAP/reference	0.82035	0.071
41DAP/reference	0.82788	0.164
42DAP/reference	0.77611	0.011
43DAP/reference	0.78333	0.032
47DAP/reference	0.87752	0.062
52DAP/reference	0.70821	0.005
57DAP/reference	0.71181	0.01

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98015	0.526
17DAP/reference	0.80622	0.154
27DAP/reference	0.75597	0.031
39DAP/reference	0.71648	0.008
41DAP/reference	0.8117	0.035
42DAP/reference	0.92838	0.445
43DAP/reference	0.85488	0.028
47DAP/reference	0.78717	0.014
52DAP/reference	0.90452	0.433
57DAP/reference	0.79446	0.026

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.84485	0.807
26DAP/20DAP	1.61257	0.315
34DAP/26DAP	0.81892	0.356
51DAP/34DAP	1.6173	0.043
52DAP/51DAP	1.20868	0.142
53DAP/52DAP	0.86935	0.489
55DAP/53DAP	0.59424	0.023
57DAP/55DAP	1.15851	0.728
62DAP/57DAP	0.92254	0.871
68DAP/62DAP	0.96467	0.834
68DAP/14DAP	1.10377	0.936

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.76585	0.062

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.32011	0.363
Immature Eggplant/Mature Eggplant	2.37824	0.062
Ripe Pepper/Ripe Tomato	0.50464	0.293
Mature Eggplant/Ripe Tomato	0.96153	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.22029	0.536
1-1-2/M82	0.80479	1
12-2/M82	N/A	N/A
12-4/M82	1.07007	0.611
1-3/M82	0.9115
2-1-1/M82	0.84548	1
2-1/M82	N/A	N/A
2-6/M82	0.61944	0.501
3-2/M82	N/A	N/A
4-1-1/M82	0.87527
4-1/M82	N/A	N/A
4-3-2/M82	1.46806
4-3/M82	1.12864	1
5-3/M82	1.0541	1
6-2/M82	N/A	N/A
6-3/M82	0.91094
7-1/M82	0.86949
7-2/M82	0.93064
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	0.89117	1
IL7-5/WTpooled	0.57626	1
IL7-3/WTpooled	1.07271	1
IL12-4/WTpooled	0.82012	0.581
IL1-4/WTpooled	0.94224	0.834
WT/WTpooled	1.00067	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	0.87606	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.10595	0.846
DC3000/delta hrp 6h	0.9467	0.95
DC3000/delta hrp 12h	0.89549	1
DC3000/delta hrp 24h	1.33555	0.165

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.50707	0.047
DC3000 delta B/DC3000 delta AB	1.18561	0.282

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86931	1
Exp 36h	1.52935	0.693
Exp 60h	1.2052	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03929	1
Var 0h	0.77235	0.933
Var 12h I row2-row1	0.98228	0.856
Var 12h NI row2-row1	0.9924	1
Var 36h I row2-row1	0.99521	1
Var 36h NI row2-row1	1.13689	0.482
Var 60h I row2-row1	0.8989	0.582
Var 60h NI row2-row1	0.9397	1
Time course 0hI-0hNI	1.03441	0.852
Time course 12hI-12hNI	1.03511	0.738
Time course 36hI-36hNI	0.9987	0.811
Time course 60hI-60hNI	0.71556	0.009

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)	1.00918	0.798
transgenic ySAMdc/azygous control (breaker)	1.25927	0.248
transgenic ySAMdc/azygous control (red)	1.01997	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.03871	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.16458	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.83309	1
Manapal/WT (break)	0.85654	0.333
Manapal/WT (red)	0.83842	0.181