Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.2.2.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.89015	0.532
27DAP/17DAP	0.77087	0.539
39DAP/27DAP	1.11447	1
41DAP/39DAP	1.2636	0.447
42DAP/41DAP	1.20982	1
43DAP/42DAP	1.02801	0.912
47DAP/43DAP	1.30424	0.3
52DAP/47DAP	0.82849	0.554
57DAP/52DAP	0.92662	0.932

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.08741	0.814
17DAP/reference	1.06238	0.369
27DAP/reference	0.92379	0.314
39DAP/reference	1.08083	0.122
41DAP/reference	1.02974	0.808
42DAP/reference	0.9317	0.12
43DAP/reference	0.99665	0.904
47DAP/reference	0.95993	0.242
52DAP/reference	0.90974	0.057
57DAP/reference	0.90527	0.147

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.60969	0.042
27DAP/17DAP	0.77032	0.39
39DAP/27DAP	0.95639	0.616
41DAP/39DAP	0.8926	0.839
42DAP/41DAP	0.91112	0.545
43DAP/42DAP	1.21074	0.446
47DAP/43DAP	0.80827	0.239
52DAP/47DAP	0.9114	0.807
57DAP/52DAP	0.71321	0.331
57DAP/7DAP	0.83881

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.93786	0.445
17DAP/reference	1.10463	0.754
27DAP/reference	1.1265	0.16
39DAP/reference	1.01126	1
41DAP/reference	1.26987	0.637
42DAP/reference	1.06191	1
43DAP/reference	1.08891	0.241
47DAP/reference	0.99023	1
52DAP/reference	0.81679	0.115
57DAP/reference	0.88598	0.176

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21909	0.067
17DAP/reference	1.03132	0.892
27DAP/reference	0.93164	0.381
39DAP/reference	0.90611	0.227
41DAP/reference	1.00632	0.666
42DAP/reference	0.96604	0.433
43DAP/reference	1.25646	0.085
47DAP/reference	1.02577	0.731
52DAP/reference	1.12766	0.009
57DAP/reference	1.23923	0.104

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87054	0.127
17DAP/reference	1.16048	0.279
27DAP/reference	1.24547	0.057
39DAP/reference	1.0866	0.235
41DAP/reference	1.14642	0.425
42DAP/reference	0.84004	0.108
43DAP/reference	0.94088	0.468
47DAP/reference	1.03667	1
52DAP/reference	1.03913	1
57DAP/reference	0.79599	0.038

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.16676	0.966
26DAP/20DAP	3.18291
34DAP/26DAP	1.2231	1
51DAP/34DAP	1.44452	0.483
52DAP/51DAP	0.78086	1
53DAP/52DAP	1.32283	0.307
55DAP/53DAP	1.27316	0.741
57DAP/55DAP	0.91303	0.817
62DAP/57DAP	0.77235	0.681
68DAP/62DAP	0.7658	0.406
68DAP/14DAP	0.62814	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.14781	0.782

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	N/A	N/A
12-2/M82	N/A	N/A
12-4/M82	N/A	N/A
1-3/M82	N/A	N/A
2-1-1/M82	N/A	N/A
2-1/M82	N/A	N/A
2-6/M82	N/A	N/A
3-2/M82	N/A	N/A
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	N/A	N/A
5-3/M82	N/A	N/A
6-2/M82	N/A	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
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	N/A	N/A
IL2-6/WTpooled	1.1324	0.788
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	2.55231	0.362
IL12-4/WTpooled	1.13375	0.785
IL1-4/WTpooled	1.55284
WT/WTpooled	1.0012	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	1.04041

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.88684	1
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.20141	1
DC3000/delta hrp 24h	1.25732	0.69

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	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04821	1
Exp 36h	N/A	N/A
Exp 60h	1.19004	0.399

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

hybridization	ratio	FDR (corrected p value)
self-self	1.18229
Var 0h	0.995	1
Var 12h I row2-row1	1.14046
Var 12h NI row2-row1	1.20516
Var 36h I row2-row1	1.03817	1
Var 36h NI row2-row1	1.19609	1
Var 60h I row2-row1	0.76513
Var 60h NI row2-row1	0.99165	1
Time course 0hI-0hNI	1.06748	0.63
Time course 12hI-12hNI	1.05533	0.818
Time course 36hI-36hNI	1.21904	0.056
Time course 60hI-60hNI	1.21715	0.216

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)	0.81243	0.662
transgenic ySAMdc/azygous control (breaker)	0.98898	1
transgenic ySAMdc/azygous control (red)	1.16902	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0264	0.287

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.02125	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.29068	0.105
Manapal/WT (break)	1.19183	1
Manapal/WT (red)	1.07379	0.413