Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.1.17.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87785	0.475
27DAP/17DAP	0.85676	0.644
39DAP/27DAP	1.12571	0.981
41DAP/39DAP	0.8606	0.455
42DAP/41DAP	0.88048	1
43DAP/42DAP	1.01875	0.937
47DAP/43DAP	0.8047	0.41
52DAP/47DAP	1.4376	0.562
57DAP/52DAP	1.00837	0.983

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.99704	0.756
17DAP/reference	0.98852	0.819
27DAP/reference	1.17986	0.446
39DAP/reference	1.13245	0.286
41DAP/reference	0.94941	0.542
42DAP/reference	0.99271	0.44
43DAP/reference	0.93624	0.394
47DAP/reference	1.18536	0.182
52DAP/reference	1.67626	0.008
57DAP/reference	1.12562	0.344

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87	0.126
27DAP/17DAP	0.90526	0.418
39DAP/27DAP	0.86291	0.239
41DAP/39DAP	1.02086	1
42DAP/41DAP	1.06972	0.984
43DAP/42DAP	0.85301	0.045
47DAP/43DAP	1.02613	0.957
52DAP/47DAP	0.64593	0.103
57DAP/52DAP	0.96988	0.73
57DAP/7DAP	0.27266

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.74837	0.059
17DAP/reference	0.75807	0.012
27DAP/reference	0.94813	0.215
39DAP/reference	0.81997	0.023
41DAP/reference	0.79183	0.042
42DAP/reference	0.78068	0.029
43DAP/reference	0.68855	0.012
47DAP/reference	0.88817	0.168
52DAP/reference	0.7389	0.022
57DAP/reference	0.76744	0.009

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.78042	0.062
17DAP/reference	0.85984	0.149
27DAP/reference	1.17013	0.1
39DAP/reference	1.18756	0.225
41DAP/reference	1.2921	0.076
42DAP/reference	1.13715	0.153
43DAP/reference	1.02122	0.569
47DAP/reference	0.97557	0.473
52DAP/reference	1.05382	0.498
57DAP/reference	0.77117	0.008

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.84337	0.147
17DAP/reference	0.84715	0.243
27DAP/reference	0.77996	0.069
39DAP/reference	0.69495	0.037
41DAP/reference	0.8349	0.031
42DAP/reference	1.02162	0.816
43DAP/reference	1.02142	0.712
47DAP/reference	1.03981	0.901
52DAP/reference	0.76965	0.097
57DAP/reference	1.1897	0.436

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.7673	1
26DAP/20DAP	1.84649	0.102
34DAP/26DAP	0.76085	0.561
51DAP/34DAP	1.55026	0.666
52DAP/51DAP	0.89972	1
53DAP/52DAP	1.34113	0.643
55DAP/53DAP	1.23924	0.893
57DAP/55DAP	0.99	0.804
62DAP/57DAP	1.16903	0.8
68DAP/62DAP	1.68326	0.069
68DAP/14DAP	1.41733	0.051

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.38761	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.8466	0.304
Mature Green Tomato/Ripe Tomato	1.44559	0.015
Immature Eggplant/Mature Eggplant	1.40771	0.222
Ripe Pepper/Ripe Tomato	0.72326	0.293
Mature Eggplant/Ripe Tomato	0.29149	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02517	0.877
1-1-2/M82	1.13205	1
12-2/M82	0.8047
12-4/M82	0.98954	1
1-3/M82	0.72286
2-1-1/M82	0.95467
2-1/M82	0.92899
2-6/M82	1.04907
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	1.31707
4-3-2/M82	1.06291	1
4-3/M82	0.57583	0.578
5-3/M82	1.23653	0.378
6-2/M82	0.97872
6-3/M82	0.85801	0.982
7-1/M82	N/A	N/A
7-2/M82	1.08931
9-3-2/M82	1.16736

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.06858	0.493
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	1.45004	0.792
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.89129	0.834
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	0.83957	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.94235	1
DC3000/delta hrp 6h	0.94699	0.95
DC3000/delta hrp 12h	1.08156	1
DC3000/delta hrp 24h	1.23623	0.107

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.38022	0.044
DC3000 delta B/DC3000 delta AB	1.45742	0.114

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.02532	1
Exp 36h	0.87916	0.82
Exp 60h	0.81815	0.386

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

hybridization	ratio	FDR (corrected p value)
self-self	0.93595	1
Var 0h	1.47805	0.98
Var 12h I row2-row1	0.93866	0.627
Var 12h NI row2-row1	1.12183	0.649
Var 36h I row2-row1	1.35458	0.298
Var 36h NI row2-row1	1.01044	1
Var 60h I row2-row1	0.75447	0.374
Var 60h NI row2-row1	0.84545	0.866
Time course 0hI-0hNI	1.11418	0.63
Time course 12hI-12hNI	0.97177	0.855
Time course 36hI-36hNI	1.23455	0.19
Time course 60hI-60hNI	1.37674	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)	1.02949	0.571
transgenic ySAMdc/azygous control (breaker)	1.53619	0.172
transgenic ySAMdc/azygous control (red)	0.88647	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.07895	0.277

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.32605	0.14
Manapal/WT (break)	1.04599	1
Manapal/WT (red)	1.23642	0.126