Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.1.2.1

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70233	0.082
27DAP/17DAP	1.16024	0.926
39DAP/27DAP	1.91451	0.057
41DAP/39DAP	0.69031	0.087
42DAP/41DAP	1.37407	0.792
43DAP/42DAP	1.13407	0.956
47DAP/43DAP	1.00089	0.754
52DAP/47DAP	1.4037	0.608
57DAP/52DAP	1.17664	0.977

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98039	0.589
17DAP/reference	1.00218	1
27DAP/reference	1.00314	0.885
39DAP/reference	1.00389	0.941
41DAP/reference	0.99514	0.814
42DAP/reference	0.97748	0.359
43DAP/reference	1.09597	0.306
47DAP/reference	1.2112	0.006
52DAP/reference	1.10675	0.607
57DAP/reference	1.19286	0.059

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.31117	0.168
27DAP/17DAP	1.03466	1
39DAP/27DAP	1.18217	0.636
41DAP/39DAP	1.25927	0.55
42DAP/41DAP	0.97185	0.649
43DAP/42DAP	1.00254	0.928
47DAP/43DAP	1.14389	0.65
52DAP/47DAP	1.1787	0.57
57DAP/52DAP	1.2435	0.344
57DAP/7DAP	2.06958	0.365

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.49234	0.04
17DAP/reference	1.04358	0.693
27DAP/reference	1.08305	0.246
39DAP/reference	1.37822	0.053
41DAP/reference	1.26809	0.066
42DAP/reference	1.14287	0.534
43DAP/reference	1.40137	0.034
47DAP/reference	1.49939	0.025
52DAP/reference	1.83755	0.008
57DAP/reference	1.52631	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93095	0.399
17DAP/reference	0.97175	0.536
27DAP/reference	0.97162	0.467
39DAP/reference	1.00073	0.661
41DAP/reference	0.90769	0.071
42DAP/reference	0.99532	0.655
43DAP/reference	0.80786	0.044
47DAP/reference	0.98772	0.574
52DAP/reference	0.77409	0.01
57DAP/reference	0.86007	0.017

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18268	0.469
17DAP/reference	0.98548	0.668
27DAP/reference	1.13373	0.552
39DAP/reference	1.07277	0.912
41DAP/reference	1.01542	0.826
42DAP/reference	1.32036	0.099
43DAP/reference	0.98955	0.59
47DAP/reference	1.03637	1
52DAP/reference	1.39491	0.059
57DAP/reference	1.73264	0.008

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.05642	1
26DAP/20DAP	1.49067	0.196
34DAP/26DAP	0.74376	0.131
51DAP/34DAP	1.30354	0.281
52DAP/51DAP	0.89195	1
53DAP/52DAP	2.17838	0.697
55DAP/53DAP	0.90931	0.5
57DAP/55DAP	1.28204	0.324
62DAP/57DAP	1.74011
68DAP/62DAP	1.04644	0.869
68DAP/14DAP	1.60912	0.366

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.9767	0.607

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.8332	0.29
Mature Green Tomato/Ripe Tomato	0.74742	0.047
Immature Eggplant/Mature Eggplant	1.02665	1
Ripe Pepper/Ripe Tomato	0.80771	0.293
Mature Eggplant/Ripe Tomato	1.25574	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.83091	0.638
1-1-2/M82	1.19703	1
12-2/M82	1.10477	0.61
12-4/M82	1.08684	1
1-3/M82	3.33934	0.26
2-1-1/M82	0.91683	0.465
2-1/M82	0.73809	0.345
2-6/M82	0.78922	0.501
3-2/M82	1.12285	0.967
4-1-1/M82	0.9631	1
4-1/M82	1.4217	1
4-3-2/M82	0.97624	1
4-3/M82	1.33448	0.268
5-3/M82	1.04758	1
6-2/M82	0.96697	1
6-3/M82	1.0642	1
7-1/M82	0.93353	0.803
7-2/M82	1.20923	1
9-3-2/M82	1.11432	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97209	1
IL2-6/WTpooled	1.03231	1
IL7-5/WTpooled	0.97336	1
IL7-3/WTpooled	0.97554	1
IL12-4/WTpooled	0.98012	1
IL1-4/WTpooled	1.13724	1
WT/WTpooled	1.06784	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	1.27887	0.193

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89863	0.545
DC3000/delta hrp 6h	1.05866	0.978
DC3000/delta hrp 12h	1.03796	1
DC3000/delta hrp 24h	1.07242	0.728

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.23994	0.134
DC3000 delta B/DC3000 delta AB	0.91183	0.317

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.98785	1
Exp 36h	1.2439	0.489
Exp 60h	1.14301	1

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02771	1
Var 0h	0.65	1
Var 12h I row2-row1	1.12276	0.654
Var 12h NI row2-row1	1.10685	1
Var 36h I row2-row1	1.15669	0.742
Var 36h NI row2-row1	0.83503	0.45
Var 60h I row2-row1	0.42207
Var 60h NI row2-row1	0.89636	0.818
Time course 0hI-0hNI	1.08085	0.852
Time course 12hI-12hNI	1.22046	0.682
Time course 36hI-36hNI	1.55184	0.007
Time course 60hI-60hNI	2.50404	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)	0.97653	0.862
transgenic ySAMdc/azygous control (breaker)	0.80517	0.15
transgenic ySAMdc/azygous control (red)	0.91839	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.50361	0.036

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.39645	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.97035	1
Manapal/WT (break)	1.14893	0.381
Manapal/WT (red)	1.52056	0.137