Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.1.10.10

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73502	0.089
27DAP/17DAP	0.92672	0.857
39DAP/27DAP	0.95148	0.67
41DAP/39DAP	0.93302	0.724
42DAP/41DAP	0.8303	1
43DAP/42DAP	0.78251	0.456
47DAP/43DAP	0.96623	0.864
52DAP/47DAP	1.1891	0.902
57DAP/52DAP	1.12391	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03813	0.735
17DAP/reference	0.96209	0.567
27DAP/reference	0.98454	0.725
39DAP/reference	0.94139	0.565
41DAP/reference	0.79292	0.039
42DAP/reference	0.9549	0.233
43DAP/reference	1.28463	0.061
47DAP/reference	0.94751	0.322
52DAP/reference	1.0675	0.951
57DAP/reference	1.20288	0.186

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.84529	0.27
27DAP/17DAP	1.0276	0.98
39DAP/27DAP	0.83054	0.211
41DAP/39DAP	0.90311	0.713
42DAP/41DAP	1.0219	0.934
43DAP/42DAP	0.943	0.558
47DAP/43DAP	0.9626	0.846
52DAP/47DAP	1.02522	0.939
57DAP/52DAP	1.16018	0.427
57DAP/7DAP	0.80585	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.03241	0.876
17DAP/reference	0.99689	0.693
27DAP/reference	0.94089	0.303
39DAP/reference	1.05945	0.74
41DAP/reference	0.86804	0.111
42DAP/reference	0.91873	0.2
43DAP/reference	0.88604	0.079
47DAP/reference	1.03824	0.868
52DAP/reference	0.77507	0.013
57DAP/reference	0.91891	0.132

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1071	0.589
17DAP/reference	0.85964	0.195
27DAP/reference	0.85399	0.304
39DAP/reference	1.0526	0.824
41DAP/reference	0.85589	0.091
42DAP/reference	0.86359	0.081
43DAP/reference	1.04864	0.748
47DAP/reference	0.71186	0.01
52DAP/reference	0.86463	0.072
57DAP/reference	0.61267	0.014

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.15471	0.103
17DAP/reference	0.9613	0.571
27DAP/reference	0.80412	0.046
39DAP/reference	0.83677	0.028
41DAP/reference	0.88446	0.264
42DAP/reference	0.92536	0.287
43DAP/reference	0.8629	0.037
47DAP/reference	0.79389	0.066
52DAP/reference	0.77866	0.074
57DAP/reference	0.90278	0.154

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91723	1
26DAP/20DAP	1.29275	0.421
34DAP/26DAP	1.09444	1
51DAP/34DAP	1.14709	0.581
52DAP/51DAP	0.88667	1
53DAP/52DAP	0.68309	0.062
55DAP/53DAP	0.49371	0.022
57DAP/55DAP	0.72527	0.074
62DAP/57DAP	1.24998	0.081
68DAP/62DAP	1.61715	0.808
68DAP/14DAP	0.57213	0.09

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.55317	0.02

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.1354	0.058
Mature Green Tomato/Ripe Tomato	1.13815	1
Immature Eggplant/Mature Eggplant	0.84021	0.092
Ripe Pepper/Ripe Tomato	0.91476	0.224
Mature Eggplant/Ripe Tomato	2.59753	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.3584	0.551
1-1-2/M82	1.03372	1
12-2/M82	N/A	N/A
12-4/M82	1.18783	1
1-3/M82	0.64576	0.378
2-1-1/M82	0.6888	0.465
2-1/M82	0.84738	N/A
2-6/M82	1.14322	1
3-2/M82	1.00216	N/A
4-1-1/M82	1.19907	N/A
4-1/M82	0.89511	N/A
4-3-2/M82	0.65733	N/A
4-3/M82	0.5877	0.509
5-3/M82	0.84556	0.642
6-2/M82	1.33457	N/A
6-3/M82	1.08061	1
7-1/M82	0.87665	N/A
7-2/M82	1.03424	1
9-3-2/M82	1.14123	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.29126	N/A
IL2-6/WTpooled	1.1055	1
IL7-5/WTpooled	1.42748	N/A
IL7-3/WTpooled	1.17937	1
IL12-4/WTpooled	0.93203	0.581
IL1-4/WTpooled	1.0849	1
WT/WTpooled	0.93558	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	0.95702	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.28563	0.656
DC3000/delta hrp 6h	0.91682	0.95
DC3000/delta hrp 12h	0.96776	1
DC3000/delta hrp 24h	0.845	0.145

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88911	0.436
DC3000 delta B/DC3000 delta AB	0.90784	0.497

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.84515	1
Exp 36h	1.01865	1
Exp 60h	0.85114	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	1.03739	1
Var 0h	1.25388	0.936
Var 12h I row2-row1	1.14302	0.544
Var 12h NI row2-row1	1.3674	0.235
Var 36h I row2-row1	0.96727	0.313
Var 36h NI row2-row1	1.06155	1
Var 60h I row2-row1	0.70885	0.287
Var 60h NI row2-row1	1.1709	0.904
Time course 0hI-0hNI	1.01724	1
Time course 12hI-12hNI	0.88588	0.144
Time course 36hI-36hNI	0.87882	0.052
Time course 60hI-60hNI	1.05519	1

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)	0.88231	0.32
transgenic ySAMdc/azygous control (breaker)	0.74517	0.15
transgenic ySAMdc/azygous control (red)	1.25266	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94019	0.27

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.00658	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.09893	1
Manapal/WT (break)	1.89049	0.183
Manapal/WT (red)	1.16172	0.413