Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.4.4.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.63906	0.11
27DAP/17DAP	0.9933	0.928
39DAP/27DAP	1.74977	0.182
41DAP/39DAP	1.04253	0.814
42DAP/41DAP	0.9335	1
43DAP/42DAP	1.14112	0.991
47DAP/43DAP	0.97145	0.754
52DAP/47DAP	1.17814	0.851
57DAP/52DAP	1.30509	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.14778	0.29
17DAP/reference	0.73082	0.01
27DAP/reference	1.09714	0.52
39DAP/reference	1.1068	0.465
41DAP/reference	0.96365	0.814
42DAP/reference	1.06173	1
43DAP/reference	0.86744	0.538
47DAP/reference	1.06741	0.541
52DAP/reference	0.78361	0.089
57DAP/reference	0.76905

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.87102	0.099
27DAP/17DAP	1.12377	0.411
39DAP/27DAP	1.08409	0.46
41DAP/39DAP	0.96513	0.934
42DAP/41DAP	1.00037	0.87
43DAP/42DAP	1.20618	0.028
47DAP/43DAP	0.93284	0.428
52DAP/47DAP	0.99876	0.97
57DAP/52DAP	0.92691	0.359
57DAP/7DAP	0.92165	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98097	0.613
17DAP/reference	0.94816	0.447
27DAP/reference	0.76328	0.058
39DAP/reference	0.86483	0.095
41DAP/reference	0.89809	0.223
42DAP/reference	1.14352	0.534
43DAP/reference	1.05577	1
47DAP/reference	1.1055	0.395
52DAP/reference	1.02508	1
57DAP/reference	0.96809	0.443

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.07517	0.915
17DAP/reference	0.87042	0.056
27DAP/reference	0.9618	0.452
39DAP/reference	0.99884	0.702
41DAP/reference	1.21215	0.657
42DAP/reference	0.97407	0.392
43DAP/reference	0.93781	0.352
47DAP/reference	1.12314	0.116
52DAP/reference	0.88153	0.055
57DAP/reference	0.96444	0.46

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83442	0.112
17DAP/reference	0.83923	0.281
27DAP/reference	0.94978
39DAP/reference	0.70393	0.025
41DAP/reference	1.24329	0.357
42DAP/reference	1.0264	1
43DAP/reference	1.12086	0.815
47DAP/reference	0.97121	0.409
52DAP/reference	0.79757	0.141
57DAP/reference	0.94205	0.366

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.30157	0.966
26DAP/20DAP	1.04791	0.839
34DAP/26DAP	0.9485	0.861
51DAP/34DAP	0.87742	0.109
52DAP/51DAP	0.99125	1
53DAP/52DAP	1.11946	0.37
55DAP/53DAP	0.98453	0.852
57DAP/55DAP	1.114	0.969
62DAP/57DAP	1.32006	0.445
68DAP/62DAP	1.16993	0.827
68DAP/14DAP	1.58789	0.419

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.18919	0.047

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	4.5168	0.058
Mature Green Tomato/Ripe Tomato	2.06468	0.025
Immature Eggplant/Mature Eggplant	5.33414	0.05
Ripe Pepper/Ripe Tomato	0.50635	0.224
Mature Eggplant/Ripe Tomato	4.03858	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.35566	0.591
1-1-2/M82	1.02604	1
12-2/M82	0.87446	0.955
12-4/M82	1.05255	1
1-3/M82	N/A	N/A
2-1-1/M82	1.13688	0.764
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	1.85617	0.426
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	2.19993
4-3/M82	1.48437
5-3/M82	0.78677	0.642
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	0.73191	0.408
7-2/M82	N/A	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	2.83052	0.277
IL2-6/WTpooled	2.31999	0.419
IL7-5/WTpooled	1.66091	0.52
IL7-3/WTpooled	2.48712	0.362
IL12-4/WTpooled	2.07111	0.557
IL1-4/WTpooled	1.25749	1
WT/WTpooled	0.8095	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	1.216	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93183	1
DC3000/delta hrp 6h	0.81504	0.95
DC3000/delta hrp 12h	0.83086	1
DC3000/delta hrp 24h	3.40896	0.037

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.8639	0.056
DC3000 delta B/DC3000 delta AB	0.83749	0.117

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.0352	1
Exp 36h	1.21778	0.693
Exp 60h	1.35306	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99965
Var 0h	0.37034	1
Var 12h I row2-row1	0.91641	0.363
Var 12h NI row2-row1	1.08525	1
Var 36h I row2-row1	1.02802	1
Var 36h NI row2-row1	1.06884	1
Var 60h I row2-row1	0.84401
Var 60h NI row2-row1	1.11884	0.904
Time course 0hI-0hNI	0.96299	0.675
Time course 12hI-12hNI	0.9623	0.698
Time course 36hI-36hNI	0.93415	0.33
Time course 60hI-60hNI	0.97043	0.646

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)	0.96586	0.529
transgenic ySAMdc/azygous control (breaker)	1.09377	1
transgenic ySAMdc/azygous control (red)	1.03898	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.12872	0.334

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.98547	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.38366	0.096
Manapal/WT (break)	0.79029	1
Manapal/WT (red)	1.36789	0.222