Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.2.7.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.98966	0.77
27DAP/17DAP	0.93137	0.876
39DAP/27DAP	0.80124	0.392
41DAP/39DAP	0.91998	0.641
42DAP/41DAP	0.92202	1
43DAP/42DAP	0.99975	0.937
47DAP/43DAP	1.03248	0.979
52DAP/47DAP	0.90609	0.711
57DAP/52DAP	0.97222	0.957

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04293	0.76
17DAP/reference	1.14734	0.166
27DAP/reference	1.8277	0.008
39DAP/reference	1.35941	0.111
41DAP/reference	1.08291	0.714
42DAP/reference	0.87338	0.012
43DAP/reference	0.90355	0.098
47DAP/reference	0.88456	0.018
52DAP/reference	0.92771	0.167
57DAP/reference	0.89829	0.071

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.02297	0.947
27DAP/17DAP	1.07212	0.761
39DAP/27DAP	0.75585	0.102
41DAP/39DAP	1.15353	0.682
42DAP/41DAP	1.10367	0.886
43DAP/42DAP	0.47989	0.022
47DAP/43DAP	1.00589	1
52DAP/47DAP	0.97945	0.919
57DAP/52DAP	0.88636	0.225
57DAP/7DAP	0.5815	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.77215	0.024
17DAP/reference	1.40344	0.01
27DAP/reference	1.18136	0.03
39DAP/reference	1.0832	0.297
41DAP/reference	1.11264	0.539
42DAP/reference	1.07508	0.686
43DAP/reference	0.84109	0.076
47DAP/reference	1.05577	0.776
52DAP/reference	0.93545	0.304
57DAP/reference	0.66373	0.008

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.00534	0.993
17DAP/reference	1.09555	0.186
27DAP/reference	1.15759	0.244
39DAP/reference	1.16515	0.355
41DAP/reference	0.96641	0.364
42DAP/reference	1.07481	0.422
43DAP/reference	0.88789	0.175
47DAP/reference	0.97723	0.423
52DAP/reference	1.01363	0.938
57DAP/reference	0.83581	0.054

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.27557	0.149
17DAP/reference	1.07971	0.45
27DAP/reference	1.20632	0.111
39DAP/reference	1.31435	0.011
41DAP/reference	1.12956	0.162
42DAP/reference	0.78018	0.071
43DAP/reference	0.9249	0.305
47DAP/reference	0.84833	0.009
52DAP/reference	0.8676	0.277
57DAP/reference	0.8669	0.05

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.07117	0.966
26DAP/20DAP	1.31547	0.228
34DAP/26DAP	0.86281	0.472
51DAP/34DAP	0.73886	0.059
52DAP/51DAP	0.99104	1
53DAP/52DAP	0.83629	0.186
55DAP/53DAP	1.00939	0.991
57DAP/55DAP	1.1103	0.71
62DAP/57DAP	0.85785	0.681
68DAP/62DAP	0.69778	0.7
68DAP/14DAP	0.54548	0.121

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.8446	0.087

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	6.17731	0.058
Mature Green Tomato/Ripe Tomato	6.6653	0.016
Immature Eggplant/Mature Eggplant	1.28157	0.058
Ripe Pepper/Ripe Tomato	1.40017	1
Mature Eggplant/Ripe Tomato	4.40412	0.268

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	0.6195
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	0.84607
4-1-1/M82	N/A	N/A
4-1/M82	N/A	N/A
4-3-2/M82	0.98472
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	0.76872	0.247
IL2-6/WTpooled	0.84021	0.348
IL7-5/WTpooled	0.82326	1
IL7-3/WTpooled	0.7278	0.31
IL12-4/WTpooled	0.85588	0.71
IL1-4/WTpooled	0.84824	0.699
WT/WTpooled	0.95847	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	0.97663	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.89161	1
DC3000/delta hrp 6h	1.02326	0.95
DC3000/delta hrp 12h	1.03515	1
DC3000/delta hrp 24h	0.60673	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.55347	0.042
DC3000 delta B/DC3000 delta AB	0.55518	0.02

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

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

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98978	1
Var 0h	0.92037	1
Var 12h I row2-row1	0.68773	0.338
Var 12h NI row2-row1	1.00462	1
Var 36h I row2-row1	0.78191	1
Var 36h NI row2-row1	1.10518	1
Var 60h I row2-row1	1.30611	0.543
Var 60h NI row2-row1	0.92909	1
Time course 0hI-0hNI	0.97697	0.917
Time course 12hI-12hNI	0.99411	1
Time course 36hI-36hNI	0.90818	0.086
Time course 60hI-60hNI	0.19867	0.005

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)	0.99591	0.931
transgenic ySAMdc/azygous control (breaker)	0.58283	0.131
transgenic ySAMdc/azygous control (red)	0.87092	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.05642	0.247

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83906	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.8326	0.172
Manapal/WT (break)	1.00397	1
Manapal/WT (red)	1.30469	0.222