Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.2.13.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.07566	0.838
27DAP/17DAP	1.51822	0.601
39DAP/27DAP	0.96179	0.719
41DAP/39DAP	1.02151	0.824
42DAP/41DAP	1.06232	0.949
43DAP/42DAP	0.91872	0.864
47DAP/43DAP	1.31912	0.502
52DAP/47DAP	1.18428	0.78
57DAP/52DAP	0.88487	0.872

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.9853	0.63
17DAP/reference	1.0214	0.585
27DAP/reference	0.96464	0.369
39DAP/reference	1.02042	0.664
41DAP/reference	0.98164	0.542
42DAP/reference	0.88982	0.013
43DAP/reference	0.90044	0.211
47DAP/reference	0.9459	0.083
52DAP/reference	0.89581	0.162
57DAP/reference	0.90905	0.156

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92302	0.496
27DAP/17DAP	1.09797	0.872
39DAP/27DAP	1.22489	0.231
41DAP/39DAP	1.18947	0.579
42DAP/41DAP	0.97074	0.732
43DAP/42DAP	1.18765	0.017
47DAP/43DAP	1.14915	0.135
52DAP/47DAP	0.87874	0.284
57DAP/52DAP	0.96206	0.678
57DAP/7DAP	1.09652	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93875	0.326
17DAP/reference	0.93414	0.22
27DAP/reference	1.01825	0.974
39DAP/reference	0.94136	0.083
41DAP/reference	0.88052	0.064
42DAP/reference	0.92468	0.2
43DAP/reference	0.88746	0.151
47DAP/reference	0.87303	0.222
52DAP/reference	0.80436	0.033
57DAP/reference	0.76639	0.022

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.10432	0.41
17DAP/reference	0.99805	0.766
27DAP/reference	1.0182	0.79
39DAP/reference	0.93107	0.314
41DAP/reference	0.86544	0.052
42DAP/reference	0.93397	0.212
43DAP/reference	1.17851	0.154
47DAP/reference	1.02286	0.675
52DAP/reference	0.96003	0.407
57DAP/reference	1.24236	0.135

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.91737	0.087
17DAP/reference	1.1147	0.347
27DAP/reference	1.1914	0.046
39DAP/reference	1.13341	0.084
41DAP/reference	1.19937	0.115
42DAP/reference	1.02483	0.802
43DAP/reference	0.80565	0.035
47DAP/reference	0.90788	0.231
52DAP/reference	1.64027	0.436
57DAP/reference	0.80473	0.019

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06547	1
26DAP/20DAP	0.84578
34DAP/26DAP	1.53383	0.819
51DAP/34DAP	2.10153	0.062
52DAP/51DAP	0.82534	0.151
53DAP/52DAP	0.95817	0.817
55DAP/53DAP	0.92696	0.233
57DAP/55DAP	1.18331	0.61
62DAP/57DAP	1.10541	0.767
68DAP/62DAP	0.87921	0.722
68DAP/14DAP	0.53942	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.97798	0.607

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.52956
Mature Green Tomato/Ripe Tomato	0.29159
Immature Eggplant/Mature Eggplant	3.9138	0.056
Ripe Pepper/Ripe Tomato	0.50076	0.293
Mature Eggplant/Ripe Tomato	0.13001	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.04008	1
1-1-2/M82	1.14303	1
12-2/M82	1.03365	1
12-4/M82	1.07064
1-3/M82	0.89169	0.378
2-1-1/M82	N/A	N/A
2-1/M82	0.89274	0.74
2-6/M82	0.89485	1
3-2/M82	N/A	N/A
4-1-1/M82	0.83679	0.668
4-1/M82	1.18328
4-3-2/M82	1.01613	1
4-3/M82	1.77074	0.268
5-3/M82	1.00761	1
6-2/M82	0.5715
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	1.04717	1
9-3-2/M82	1.10956	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.83925	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.96009	1
IL12-4/WTpooled	0.79064	0.581
IL1-4/WTpooled	0.80402	0.699
WT/WTpooled	1.03505	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	1.38285	0.154

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01465	0.921
DC3000/delta hrp 6h	0.94772	0.95
DC3000/delta hrp 12h	1.04274	1
DC3000/delta hrp 24h	1.08337	0.453

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	1.20183	0.437

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.06493	1
Exp 36h	1.08333	1
Exp 60h	1.22693	0.237

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

hybridization	ratio	FDR (corrected p value)
self-self	1.06202	1
Var 0h	1.00634	1
Var 12h I row2-row1	1.27258	0.222
Var 12h NI row2-row1	0.93748	0.713
Var 36h I row2-row1	0.92977	0.805
Var 36h NI row2-row1	0.98082	0.791
Var 60h I row2-row1	0.96521	0.285
Var 60h NI row2-row1	1.37691	0.904
Time course 0hI-0hNI	1.11313	0.603
Time course 12hI-12hNI	1.16897	0.091
Time course 36hI-36hNI	1.45717	0.006
Time course 60hI-60hNI	2.91771	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)	0.99061	0.862
transgenic ySAMdc/azygous control (breaker)	0.69242	0.139
transgenic ySAMdc/azygous control (red)	1.0096	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02445	0.273

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.75377	0.241

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.39589	0.307
Manapal/WT (break)	0.64431	0.299
Manapal/WT (red)	0.51254	0.181