Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.16.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.63336	0.087
27DAP/17DAP	1.01236	1
39DAP/27DAP	1.22258	0.752
41DAP/39DAP	0.98883	0.876
42DAP/41DAP	0.7814	0.774
43DAP/42DAP	0.74518	0.514
47DAP/43DAP	0.8496	0.526
52DAP/47DAP	1.17503	0.957
57DAP/52DAP	1.05067	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.02357	1
17DAP/reference	0.97416	0.63
27DAP/reference	0.97122	0.623
39DAP/reference	0.82407	0.044
41DAP/reference	0.73462	0.031
42DAP/reference	0.74023	0.001
43DAP/reference	0.93595	0.273
47DAP/reference	0.92476	0.174
52DAP/reference	1.294	0.038
57DAP/reference	1.22261	0.032

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.74858	0.228
27DAP/17DAP	1.12457	0.957
39DAP/27DAP	0.77107	0.207
41DAP/39DAP	0.97797	0.98
42DAP/41DAP	1.09192	0.559
43DAP/42DAP	1.02918	0.83
47DAP/43DAP	0.87681	0.211
52DAP/47DAP	0.84715	0.309
57DAP/52DAP	1.17398	0.552
57DAP/7DAP	0.86421	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.17758	0.11
17DAP/reference	1.05103	0.822
27DAP/reference	1.17969	0.073
39DAP/reference	1.08321	0.351
41DAP/reference	1.03416	1
42DAP/reference	0.93912	0.32
43DAP/reference	1.12065	0.256
47DAP/reference	0.99404	1
52DAP/reference	1.10477	0.058
57DAP/reference	1.05413	1

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.81032	0.012
17DAP/reference	0.90054	0.176
27DAP/reference	0.83756	0.1
39DAP/reference	0.96469	0.404
41DAP/reference	0.79187	0.01
42DAP/reference	0.92768	0.189
43DAP/reference	0.61837	0.007
47DAP/reference	0.77535	0.022
52DAP/reference	0.79282	0.013
57DAP/reference	0.74921	0.017

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15398	0.505
17DAP/reference	1.02366	1
27DAP/reference	1.02744	1
39DAP/reference	0.92821	0.271
41DAP/reference	1.07511	0.231
42DAP/reference	1.0677	0.671
43DAP/reference	1.09923	0.679
47DAP/reference	0.77058	0.019
52DAP/reference	1.14203	0.837
57DAP/reference	1.07943	0.332

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.47217	0.966
26DAP/20DAP	1.07998	0.974
34DAP/26DAP	0.95652	0.909
51DAP/34DAP	1.11682	0.581
52DAP/51DAP	0.80784	1
53DAP/52DAP	0.76215	0.097
55DAP/53DAP	0.60111	0.017
57DAP/55DAP	1.02706	0.845
62DAP/57DAP	1.37707	0.515
68DAP/62DAP	1.30318	0.845
68DAP/14DAP	0.91129	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.47299	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.22538	0.058
Mature Green Tomato/Ripe Tomato	2.05393	0.064
Immature Eggplant/Mature Eggplant	0.79547	0.081
Ripe Pepper/Ripe Tomato	1.0426	1
Mature Eggplant/Ripe Tomato	2.59277	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.18534	1
1-1-2/M82	1.01782	1
12-2/M82	1.04475	1
12-4/M82	0.86255	0.358
1-3/M82	0.95161
2-1-1/M82	0.92931	0.784
2-1/M82	1.04368
2-6/M82	1.03999	1
3-2/M82	0.68021
4-1-1/M82	0.67404	1
4-1/M82	N/A	N/A
4-3-2/M82	0.65315	0.487
4-3/M82	0.63375	0.611
5-3/M82	0.87941	1
6-2/M82	1.26703
6-3/M82	1.1173	1
7-1/M82	0.98601
7-2/M82	1.17827	1
9-3-2/M82	0.97704

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.13424	0.362
IL12-4/WTpooled	1.48713	0.557
IL1-4/WTpooled	4.56494	1
WT/WTpooled	0.99653	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	1.17795	0.193

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.15166	0.914
DC3000/delta hrp 6h	0.94146	0.95
DC3000/delta hrp 12h	0.95378	1
DC3000/delta hrp 24h	0.87269	0.077

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.86402	0.077
DC3000 delta B/DC3000 delta AB	0.86732	0.317

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.90278	1
Exp 36h	1.1097	1
Exp 60h	0.95659	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.01909	1
Var 0h	0.35644	0.933
Var 12h I row2-row1	1.16	0.544
Var 12h NI row2-row1	1.26035	0.649
Var 36h I row2-row1	0.87697	1
Var 36h NI row2-row1	1.25238	1
Var 60h I row2-row1	0.71323	0.292
Var 60h NI row2-row1	1.05527	1
Time course 0hI-0hNI	1.01483	1
Time course 12hI-12hNI	0.91737	0.303
Time course 36hI-36hNI	0.925	0.156
Time course 60hI-60hNI	1.07801	0.673

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)	1.00727	1
transgenic ySAMdc/azygous control (breaker)	0.82479	0.15
transgenic ySAMdc/azygous control (red)	1.24261	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95153	0.362

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.41109	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1251	1
Manapal/WT (break)	1.98199	0.381
Manapal/WT (red)	1.37915	0.15