Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-2.3.4.2

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.08107	0.77
27DAP/17DAP	1.10178	0.859
39DAP/27DAP	1.19973	1
41DAP/39DAP	0.88073	0.627
42DAP/41DAP	1.08191	0.954
43DAP/42DAP	1.05356	1
47DAP/43DAP	1.0246	0.95
52DAP/47DAP	1.19485	0.856
57DAP/52DAP	1.10336	0.859

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00504	1
17DAP/reference	0.96796	0.567
27DAP/reference	0.79027	0.095
39DAP/reference	0.91796	0.324
41DAP/reference	0.83535	0.085
42DAP/reference	0.90307	0.043
43DAP/reference	0.99986	0.924
47DAP/reference	0.9982	0.674
52DAP/reference	0.99404	0.668
57DAP/reference	1.11856	0.496

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04384	0.642
27DAP/17DAP	0.94972	0.537
39DAP/27DAP	1.15503	0.441
41DAP/39DAP	0.93188	0.662
42DAP/41DAP	1.02595	1
43DAP/42DAP	1.15195	0.086
47DAP/43DAP	0.97487	0.855
52DAP/47DAP	1.03133	0.907
57DAP/52DAP	1.0084	1
57DAP/7DAP	1.2086	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.22955	0.231
17DAP/reference	1.61977	0.123
27DAP/reference	1.22935	0.16
39DAP/reference	1.46999	0.026
41DAP/reference	1.28608	0.09
42DAP/reference	1.07189	0.686
43DAP/reference	1.17979	0.256
47DAP/reference	1.1198	0.458
52DAP/reference	1.46265	0.024
57DAP/reference	1.43156	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.0411	0.943
17DAP/reference	0.89328	0.189
27DAP/reference	0.85186	0.123
39DAP/reference	0.96373	0.497
41DAP/reference	0.97419	0.422
42DAP/reference	0.85506	0.028
43DAP/reference	0.747	0.033
47DAP/reference	0.864	0.173
52DAP/reference	1.0701	0.988
57DAP/reference	0.90247	0.194

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.13719	0.616
17DAP/reference	1.01169	0.87
27DAP/reference	1.48607	0.048
39DAP/reference	1.01881	0.693
41DAP/reference	1.24891	0.343
42DAP/reference	0.94529	0.552
43DAP/reference	1.2442	0.388
47DAP/reference	0.83983	0.031
52DAP/reference	1.07306	0.714
57DAP/reference	0.98019	0.602

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97744	1
26DAP/20DAP	1.09981	0.689
34DAP/26DAP	1.04429	1
51DAP/34DAP	0.91532	0.579
52DAP/51DAP	1.04972	0.708
53DAP/52DAP	0.9545	0.758
55DAP/53DAP	0.94204	0.663
57DAP/55DAP	1.1893	0.728
62DAP/57DAP	1.77332	0.393
68DAP/62DAP	1.10413	0.939
68DAP/14DAP	1.48928	0.265

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.89308	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.60063	0.162
Mature Green Tomato/Ripe Tomato	1.67522	0.106
Immature Eggplant/Mature Eggplant	1.50243	0.065
Ripe Pepper/Ripe Tomato	1.38081	0.256
Mature Eggplant/Ripe Tomato	1.44456	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.12297	0.877
1-1-2/M82	0.96594	1
12-2/M82	N/A	N/A
12-4/M82	0.91212	0.619
1-3/M82	N/A	N/A
2-1-1/M82	1.04813	N/A
2-1/M82	N/A	N/A
2-6/M82	1.03459	0.695
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	0.93073	N/A
4-3-2/M82	1.26752	N/A
4-3/M82	N/A	N/A
5-3/M82	1.01025	1
6-2/M82	1.40855	1
6-3/M82	N/A	N/A
7-1/M82	1.07095	N/A
7-2/M82	1.0731	N/A
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.01801	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	0.94302	N/A
IL12-4/WTpooled	0.80045	0.71
IL1-4/WTpooled	1.0488	N/A
WT/WTpooled	1.11774	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	0.83601	0.209

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.95762	1
DC3000/delta hrp 6h	1.07593	1
DC3000/delta hrp 12h	0.89267	1
DC3000/delta hrp 24h	0.95146	0.7

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.88069	N/A
DC3000 delta B/DC3000 delta AB	0.84675	0.157

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	N/A	N/A
Exp 36h	0.98805	1
Exp 60h	1.00907	1

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	1.22216	0.216
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	N/A	N/A
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	N/A	N/A
Time course 60hI-60hNI	N/A	N/A

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)	1.08732	0.36
transgenic ySAMdc/azygous control (breaker)	1.40956	0.172
transgenic ySAMdc/azygous control (red)	1.13574	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99238	0.673

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.87739	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.00881	1
Manapal/WT (break)	1.15979	1
Manapal/WT (red)	1.09271	0.413