Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.7.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98244	0.823
27DAP/17DAP	1.22029	0.864
39DAP/27DAP	1.34225	0.453
41DAP/39DAP	1.04033	0.921
42DAP/41DAP	1.22878	0.681
43DAP/42DAP	0.93588	0.877
47DAP/43DAP	1.3211	0.349
52DAP/47DAP	0.93839	0.799
57DAP/52DAP	1.42055	0.648

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.57952	0.012
17DAP/reference	1.31098	0.108
27DAP/reference	1.37441	0.08
39DAP/reference	0.83639	0.078
41DAP/reference	0.78966	0.016
42DAP/reference	0.88903	0.003
43DAP/reference	0.86758	0.211
47DAP/reference	0.89571	0.065
52DAP/reference	0.97921	0.475
57DAP/reference	1.06446	0.548

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.76812	0.126
27DAP/17DAP	1.15835	0.557
39DAP/27DAP	0.94706	0.759
41DAP/39DAP	1.01551	1
42DAP/41DAP	1.08041	0.8
43DAP/42DAP	0.85064	0.351
47DAP/43DAP	0.90867	0.247
52DAP/47DAP	0.99971	0.97
57DAP/52DAP	0.98178	0.776
57DAP/7DAP	0.88024

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.51965	0.024
17DAP/reference	1.12898	0.297
27DAP/reference	1.06666	0.453
39DAP/reference	0.88193	0.023
41DAP/reference	1.00723	0.848
42DAP/reference	1.01189	1
43DAP/reference	1.19599	0.408
47DAP/reference	1.05131	1
52DAP/reference	1.20801	0.018
57DAP/reference	0.89823	0.093

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.43708	0.177
17DAP/reference	1.79569	0.007
27DAP/reference	1.31701	0.208
39DAP/reference	0.90187	0.189
41DAP/reference	0.91902	0.141
42DAP/reference	1.12825	0.317
43DAP/reference	0.84314	0.108
47DAP/reference	0.74271	0.058
52DAP/reference	0.69669	0.007
57DAP/reference	0.67326	0.005

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2427	0.031
17DAP/reference	1.25831	0.166
27DAP/reference	1.04784	0.805
39DAP/reference	1.02549	0.858
41DAP/reference	0.93601	0.119
42DAP/reference	0.9114	0.22
43DAP/reference	0.94856	0.365
47DAP/reference	0.72509	0.007
52DAP/reference	0.91362	0.472
57DAP/reference	0.95016	0.339

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.25864	0.966
26DAP/20DAP	0.80881	0.512
34DAP/26DAP	1.10293	1
51DAP/34DAP	0.79291	0.176
52DAP/51DAP	1.0746	0.556
53DAP/52DAP	0.94583	0.767
55DAP/53DAP	1.03836	0.981
57DAP/55DAP	1.38099	0.188
62DAP/57DAP	0.83053	0.466
68DAP/62DAP	0.97018	0.834
68DAP/14DAP	1.03096	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0186	0.865

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.74476	0.058
Mature Green Tomato/Ripe Tomato	1.57915	0.036
Immature Eggplant/Mature Eggplant	0.8951	0.292
Ripe Pepper/Ripe Tomato	1.04863	1
Mature Eggplant/Ripe Tomato	1.10098	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.16763	1
1-1-2/M82	1.14527	1
12-2/M82	0.97549	0.955
12-4/M82	0.98076	0.33
1-3/M82	N/A	N/A
2-1-1/M82	0.84094
2-1/M82	1.35797	1
2-6/M82	0.96331	1
3-2/M82	1.10072	0.388
4-1-1/M82	0.66682
4-1/M82	0.60608
4-3-2/M82	1.15192
4-3/M82	1.3472	1
5-3/M82	1.11957	1
6-2/M82	0.9641
6-3/M82	0.67625	0.857
7-1/M82	0.79716
7-2/M82	1.04377	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.23449	0.277
IL2-6/WTpooled	1.19198	0.456
IL7-5/WTpooled	1.19352	1
IL7-3/WTpooled	0.90293	0.418
IL12-4/WTpooled	1.09442	0.737
IL1-4/WTpooled	0.95597	1
WT/WTpooled	0.975	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	1.02283	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.15371	0.894
DC3000/delta hrp 6h	1.00777	1
DC3000/delta hrp 12h	0.89551	1
DC3000/delta hrp 24h	1.14879	0.322

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.02621	1
DC3000 delta B/DC3000 delta AB	1.12877	0.381

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.99387	1
Exp 36h	0.81699	0.504
Exp 60h	0.80281	0.258

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

hybridization	ratio	FDR (corrected p value)
self-self	1.16473	1
Var 0h	0.80127	0.933
Var 12h I row2-row1	1.06318	0.654
Var 12h NI row2-row1	1.1715	1
Var 36h I row2-row1	1.94075	0.908
Var 36h NI row2-row1	0.90666	0.478
Var 60h I row2-row1	0.77094	0.287
Var 60h NI row2-row1	1.0467	0.904
Time course 0hI-0hNI	1.01354	1
Time course 12hI-12hNI	0.96597	0.836
Time course 36hI-36hNI	1.11055	0.218
Time course 60hI-60hNI	1.63193	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)	0.81108	0.315
transgenic ySAMdc/azygous control (breaker)	0.60467	0.137
transgenic ySAMdc/azygous control (red)	1.04215	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.94927	0.404

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.76574	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95675	1
Manapal/WT (break)	0.89732	1
Manapal/WT (red)	0.97939	0.424