Tomato Functional Genomics Database (TFGD)

Expression of 1-1-7.2.3.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2552	0.188
27DAP/17DAP	1.12036	0.889
39DAP/27DAP	1.25319	0.52
41DAP/39DAP	0.88552	0.543
42DAP/41DAP	1.82591	0.458
43DAP/42DAP	1.10178	1
47DAP/43DAP	1.18761	0.776
52DAP/47DAP	0.99773	0.842
57DAP/52DAP	1.21638	0.873

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.06516	0.76
17DAP/reference	1.06198	0.33
27DAP/reference	0.97403	0.642
39DAP/reference	1.06009	0.386
41DAP/reference	1.19072	0.014
42DAP/reference	0.65647	0.268
43DAP/reference	1.35937
47DAP/reference	4.59532	0.015
52DAP/reference	0.88977	0.393
57DAP/reference	0.59068	0.21

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85329	0.135
27DAP/17DAP	0.98794	0.887
39DAP/27DAP	0.92975	0.594
41DAP/39DAP	0.97108	0.98
42DAP/41DAP	1.03676	0.887
43DAP/42DAP	1.04138	0.212
47DAP/43DAP	0.86745	0.439
52DAP/47DAP	1.00367	0.979
57DAP/52DAP	0.9075	0.56
57DAP/7DAP	1.03988	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97708	0.361
17DAP/reference	1.02731	0.525
27DAP/reference	1.00393	1
39DAP/reference	1.01273	0.634
41DAP/reference	0.90768	0.098
42DAP/reference	0.92617	0.136
43DAP/reference	1.00337	0.802
47DAP/reference	1.19692	0.173
52DAP/reference	0.94482	0.232
57DAP/reference	0.94615	0.137

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96723	0.706
17DAP/reference	1.08946	1
27DAP/reference	1.35935	0.126
39DAP/reference	1.3267	0.051
41DAP/reference	1.28771	0.07
42DAP/reference	1.31404	0.066
43DAP/reference	1.14808	0.126
47DAP/reference	1.28588	0.026
52DAP/reference	1.36591	0.034
57DAP/reference	1.09423	0.688

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.96962	0.29
17DAP/reference	1.09301	0.333
27DAP/reference	1.07599	0.061
39DAP/reference	1.03098	0.563
41DAP/reference	1.08359	0.104
42DAP/reference	1.1458	0.382
43DAP/reference	1.22384	0.1
47DAP/reference	1.43305	0.68
52DAP/reference	1.11502	0.583
57DAP/reference	1.24792	0.086

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.99843	1
26DAP/20DAP	0.96262	1
34DAP/26DAP	1.03763	1
51DAP/34DAP	1.14242	0.565
52DAP/51DAP	0.95767	1
53DAP/52DAP	1.07047	0.902
55DAP/53DAP	15.3871	0.689
57DAP/55DAP	0.8864	0.619
62DAP/57DAP	0.84596	0.004
68DAP/62DAP	1.29987	0.977
68DAP/14DAP	0.65551

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.15303	0.558

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70657	0.228
Mature Green Tomato/Ripe Tomato	1.11823	1
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	0.93824	1
Mature Eggplant/Ripe Tomato	0.60223	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.57884
1-1-2/M82	1.32806	1
12-2/M82	N/A	N/A
12-4/M82	1.0018	1
1-3/M82	1.58339
2-1-1/M82	1.42222	1
2-1/M82	0.71385	0.74
2-6/M82	2.14424
3-2/M82	0.50424
4-1-1/M82	0.99091
4-1/M82	N/A	N/A
4-3-2/M82	1.33711	0.508
4-3/M82	1.64793	1
5-3/M82	0.76398	0.49
6-2/M82	N/A	N/A
6-3/M82	0.68793
7-1/M82	N/A	N/A
7-2/M82	N/A	N/A
9-3-2/M82	1.18829

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.90155	1
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.03224	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	1.17752
WT/WTpooled	N/A	N/A

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	1.43807	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89821	1
DC3000/delta hrp 6h	1.05745	1
DC3000/delta hrp 12h	1.07371	1
DC3000/delta hrp 24h	1.25555	0.06

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	1.42975	0.332

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.88117	0.328
Exp 36h	0.71155	0.504
Exp 60h	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	1.08079	0.98
Var 12h I row2-row1	0.7947	0.328
Var 12h NI row2-row1	1.08067	1
Var 36h I row2-row1	0.96321	1
Var 36h NI row2-row1	1.40021	1
Var 60h I row2-row1	1.36228
Var 60h NI row2-row1	1.19569	0.904
Time course 0hI-0hNI	0.95355	0.87
Time course 12hI-12hNI	1.00131	1
Time course 36hI-36hNI	0.71795	0.023
Time course 60hI-60hNI	0.48242	0.009

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)	0.94803	0.289
transgenic ySAMdc/azygous control (breaker)	0.86742	0.251
transgenic ySAMdc/azygous control (red)	0.92964	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.16411	0.035

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.09588	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.12944	0.105
Manapal/WT (break)	1.10464	0.381
Manapal/WT (red)	1.41325	0.413