Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-1.2.4.19

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98995	0.788
27DAP/17DAP	1.06014	0.885
39DAP/27DAP	0.7925	0.41
41DAP/39DAP	0.86979	0.591
42DAP/41DAP	0.99566	1
43DAP/42DAP	1.37651	0.252
47DAP/43DAP	0.99535	0.804
52DAP/47DAP	1.12137	0.984
57DAP/52DAP	0.97715	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80924	0.036
17DAP/reference	0.81155	0.12
27DAP/reference	0.78534	0.275
39DAP/reference	0.89742	0.081
41DAP/reference	0.69217	0.267
42DAP/reference	0.87069	0.088
43DAP/reference	0.65419	0.36
47DAP/reference	0.95182	0.392
52DAP/reference	1.26809	0.766
57DAP/reference	0.32307	N/A

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.47933	0.142
27DAP/17DAP	0.88375	0.206
39DAP/27DAP	0.68986	0.194
41DAP/39DAP	0.93927	0.696
42DAP/41DAP	0.9049	0.572
43DAP/42DAP	1.15059	0.297
47DAP/43DAP	0.8531	0.214
52DAP/47DAP	0.84777	0.617
57DAP/52DAP	0.9615	0.685
57DAP/7DAP	1.20585	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.30292	0.213
17DAP/reference	1.28929	0.077
27DAP/reference	1.0402	0.974
39DAP/reference	1.20409	0.267
41DAP/reference	1.26074	0.09
42DAP/reference	1.03848	1
43DAP/reference	1.26317	0.148
47DAP/reference	1.06932	0.98
52DAP/reference	1.00182	0.74
57DAP/reference	1.10024	0.117

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.19633	0.559
17DAP/reference	1.00645	0.851
27DAP/reference	0.8478	0.06
39DAP/reference	1.02059	0.824
41DAP/reference	0.96559	0.364
42DAP/reference	0.83877	0.169
43DAP/reference	0.67422	0.011
47DAP/reference	0.76494	0.048
52DAP/reference	0.94003	0.28
57DAP/reference	0.77748	0.026

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	5.28588	0.021
17DAP/reference	1.5304	0.166
27DAP/reference	1.20471	0.216
39DAP/reference	1.25339	0.227
41DAP/reference	1.20834	0.257
42DAP/reference	6.52183	0.011
43DAP/reference	5.00538	0.013
47DAP/reference	1.33629	0.081
52DAP/reference	5.43829	0.067
57DAP/reference	2.08829	0.111

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.15747	0.586
26DAP/20DAP	0.92724	1
34DAP/26DAP	N/A	N/A
51DAP/34DAP	1.3887	0.044
52DAP/51DAP	0.85384	1
53DAP/52DAP	0.78231	0.371
55DAP/53DAP	0.6291	0.181
57DAP/55DAP	1.19806	0.854
62DAP/57DAP	0.93834	0.994
68DAP/62DAP	1.23091	0.148
68DAP/14DAP	1.09659	0.87

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.76743	0.137

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.85837	0.329
Mature Green Tomato/Ripe Tomato	2.07472	0.015
Immature Eggplant/Mature Eggplant	0.87985	0.105
Ripe Pepper/Ripe Tomato	1.96052	1
Mature Eggplant/Ripe Tomato	1.59448	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.60898	0.536
1-1-2/M82	1.0336	1
12-2/M82	0.92432	N/A
12-4/M82	0.89246	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	1.73424	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	1.37178	N/A
5-3/M82	0.70489	N/A
6-2/M82	2.29088	N/A
6-3/M82	N/A	N/A
7-1/M82	N/A	N/A
7-2/M82	2.12657	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	1.64995	N/A
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.18913	1
IL12-4/WTpooled	0.91396	1
IL1-4/WTpooled	1.16618	1
WT/WTpooled	1.08339	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	0.81635	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.90517	1
DC3000/delta hrp 6h	0.91859	0.95
DC3000/delta hrp 12h	0.76326	1
DC3000/delta hrp 24h	0.61821	0.035

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.54713	0.027
DC3000 delta B/DC3000 delta AB	0.50921	0.021

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.76961	0.328
Exp 36h	0.83409	0.661
Exp 60h	0.75308	0.253

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

hybridization	ratio	FDR (corrected p value)
self-self	1.02339	1
Var 0h	1.01039	1
Var 12h I row2-row1	0.91725	0.705
Var 12h NI row2-row1	1.16584	1
Var 36h I row2-row1	1.0526	1
Var 36h NI row2-row1	1.25994	0.482
Var 60h I row2-row1	0.81774	N/A
Var 60h NI row2-row1	1.28974	0.904
Time course 0hI-0hNI	0.94824	0.623
Time course 12hI-12hNI	0.97466	0.86
Time course 36hI-36hNI	0.84572	0.081
Time course 60hI-60hNI	0.19714	0.006

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)	1.05068	0.431
transgenic ySAMdc/azygous control (breaker)	0.67573	0.122
transgenic ySAMdc/azygous control (red)	1.44048	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.89644	0.22

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.82263	0.239

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	4.68634	0.083
Manapal/WT (break)	2.91902	0.183
Manapal/WT (red)	2.27762	0.126