Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.1.11.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03633	0.76
27DAP/17DAP	2.01345	0.511
39DAP/27DAP	0.90957	0.641
41DAP/39DAP	0.70732	0.247
42DAP/41DAP	1.53723	0.336
43DAP/42DAP	0.99959	0.937
47DAP/43DAP	0.94192	0.76
52DAP/47DAP	2.48585	0.108
57DAP/52DAP	0.62236	0.513

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07579	0.662
17DAP/reference	0.79323	0.01
27DAP/reference	1.11779	0.735
39DAP/reference	0.76379	0.042
41DAP/reference	0.78498	0.026
42DAP/reference	1.51014	0.001
43DAP/reference	0.88969	0.17
47DAP/reference	0.99167	0.602
52DAP/reference	1.12448	0.453
57DAP/reference	0.94754	0.294

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.23188	0.662
27DAP/17DAP	1.09141	0.798
39DAP/27DAP	0.95958	0.784
41DAP/39DAP	1.17822	0.612
42DAP/41DAP	0.91931	0.503
43DAP/42DAP	1.16282	0.072
47DAP/43DAP	1.08389	0.87
52DAP/47DAP	1.1848	0.573
57DAP/52DAP	1.46383	0.192
57DAP/7DAP	1.69665

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95418	0.402
17DAP/reference	1.14275	0.162
27DAP/reference	1.03551	0.453
39DAP/reference	0.86022	0.064
41DAP/reference	0.97148	0.412
42DAP/reference	1.03475	0.889
43DAP/reference	1.58044	0.009
47DAP/reference	0.85939	0.128
52DAP/reference	1.3404	0.009
57DAP/reference	2.10467	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85844	0.17
17DAP/reference	1.31939	0.03
27DAP/reference	1.01207	0.711
39DAP/reference	1.09951	0.783
41DAP/reference	1.39605	0.022
42DAP/reference	0.96868	0.433
43DAP/reference	0.95713	0.486
47DAP/reference	1.01713	0.77
52DAP/reference	0.81611	0.011
57DAP/reference	0.99833	0.789

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80612	0.033
17DAP/reference	0.97805	0.668
27DAP/reference	1.17128	0.075
39DAP/reference	1.09997	0.365
41DAP/reference	0.88346	0.05
42DAP/reference	1.11498	0.635
43DAP/reference	1.43903	0.042
47DAP/reference	1.00218	0.708
52DAP/reference	2.07266	0.062
57DAP/reference	1.60466	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.08572	1
26DAP/20DAP	0.68482	0.317
34DAP/26DAP	1.47307	0.819
51DAP/34DAP	1.07856	0.775
52DAP/51DAP	1.1419	0.202
53DAP/52DAP	1.382	0.274
55DAP/53DAP	0.90681	0.489
57DAP/55DAP	0.61455	0.031
62DAP/57DAP	0.83695	0.088
68DAP/62DAP	1.15459	1
68DAP/14DAP	0.90447	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.98805	0.696

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.49848	0.099
Mature Green Tomato/Ripe Tomato	0.18635	0.018
Immature Eggplant/Mature Eggplant	0.90207	0.329
Ripe Pepper/Ripe Tomato	0.4917	0.224
Mature Eggplant/Ripe Tomato	0.32708	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.76742
1-1-2/M82	0.66807
12-2/M82	3.22446	0.519
12-4/M82	0.59694	0.358
1-3/M82	2.72917	0.248
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	1.57068	0.695
3-2/M82	N/A	N/A
4-1-1/M82	1.90802
4-1/M82	1.56701	0.401
4-3-2/M82	N/A	N/A
4-3/M82	1.91286
5-3/M82	0.40574	0.49
6-2/M82	3.97956
6-3/M82	1.54449	1
7-1/M82	0.43521
7-2/M82	1.73794	0.324
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.3119	0.277
IL2-6/WTpooled	1.08668	0.659
IL7-5/WTpooled	1.02561	1
IL7-3/WTpooled	0.99191	0.418
IL12-4/WTpooled	0.89397	0.543
IL1-4/WTpooled	1.30941	1
WT/WTpooled	0.95365	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	2.15514	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14932	0.846
DC3000/delta hrp 6h	1.16292	1
DC3000/delta hrp 12h	0.97821	1
DC3000/delta hrp 24h	1.12878	0.411

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	2.52598

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.00866	1
Exp 36h	0.80327	0.504
Exp 60h	1.187	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.08866	1
Var 0h	1.09021	0.98
Var 12h I row2-row1	0.96643	0.705
Var 12h NI row2-row1	1.04809	0.649
Var 36h I row2-row1	1.19871	0.742
Var 36h NI row2-row1	0.73713	0.584
Var 60h I row2-row1	1.02655	1
Var 60h NI row2-row1	0.79243	0.458
Time course 0hI-0hNI	1.21754	0.486
Time course 12hI-12hNI	1.20142	0.554
Time course 36hI-36hNI	1.60723	0.007
Time course 60hI-60hNI	11.7305	0.008

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)	1.40289	0.397
transgenic ySAMdc/azygous control (breaker)	0.44141	0.134
transgenic ySAMdc/azygous control (red)	1.03213	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08448	0.125

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.14168	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.71399	1
Manapal/WT (break)	0.75984	1
Manapal/WT (red)	0.42266	0.229