Tomato Functional Genomics Database (TFGD)

Expression of 1-1-5.3.14.17

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.73975	0.095
27DAP/17DAP	0.72335	0.149
39DAP/27DAP	0.64379	0.335
41DAP/39DAP	0.92135	0.623
42DAP/41DAP	0.73734	0.774
43DAP/42DAP	1.7633	0.066
47DAP/43DAP	0.61871	0.133
52DAP/47DAP	0.71832	0.463
57DAP/52DAP	1.0075	0.971

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26841	0.026
17DAP/reference	1.13067	0.22
27DAP/reference	1.05124	0.88
39DAP/reference	1.11441	0.593
41DAP/reference	0.85995	0.065
42DAP/reference	0.92092	0.099
43DAP/reference	0.78223	0.014
47DAP/reference	0.87137	0.03
52DAP/reference	0.80882	0.125
57DAP/reference	0.86473	0.062

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.9121	0.484
27DAP/17DAP	0.8854	0.39
39DAP/27DAP	0.56355	0.04
41DAP/39DAP	1.01029	1
42DAP/41DAP	0.84396	0.243
43DAP/42DAP	0.72511	0.026
47DAP/43DAP	0.962	0.833
52DAP/47DAP	1.43127	0.362
57DAP/52DAP	0.92807	0.587
57DAP/7DAP	0.91317

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.49013	0.044
17DAP/reference	1.10204	0.123
27DAP/reference	0.97448	0.494
39DAP/reference	1.12996	0.57
41DAP/reference	0.85537	0.035
42DAP/reference	1.01293	0.791
43DAP/reference	0.86156	0.072
47DAP/reference	0.77992	0.101
52DAP/reference	0.83281	0.049
57DAP/reference	0.83443	0.029

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24635	0.35
17DAP/reference	1.31431	0.007
27DAP/reference	1.14787	0.419
39DAP/reference	0.98237	0.509
41DAP/reference	0.84932	0.063
42DAP/reference	0.91258	0.212
43DAP/reference	0.99464	0.692
47DAP/reference	0.83442	0.054
52DAP/reference	0.86931	0.121
57DAP/reference	0.7995	0.063

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.96741	0.015
17DAP/reference	1.7385	0.019
27DAP/reference	1.19941	0.067
39DAP/reference	0.98384	0.43
41DAP/reference	0.89285	0.209
42DAP/reference	1.11229	0.576
43DAP/reference	1.05339	0.688
47DAP/reference	1.3215	0.029
52DAP/reference	0.94139	0.562
57DAP/reference	1.27616	0.214

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.12943	0.966
26DAP/20DAP	0.54534	0.317
34DAP/26DAP	1.10281	1
51DAP/34DAP	0.82054	0.571
52DAP/51DAP	1.16428	0.439
53DAP/52DAP	1.0978	0.921
55DAP/53DAP	0.96326	0.796
57DAP/55DAP	1.01275	0.969
62DAP/57DAP	1.07232	1
68DAP/62DAP	1.41201	0.626
68DAP/14DAP	0.73431	0.086

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.84393	0.175

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	2.06738	0.113
Mature Green Tomato/Ripe Tomato	18.3516	0.015
Immature Eggplant/Mature Eggplant	0.36829	0.062
Ripe Pepper/Ripe Tomato	5.91305	1
Mature Eggplant/Ripe Tomato	4.37795	0.268

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	N/A	N/A
1-1-2/M82	0.82128
12-2/M82	N/A	N/A
12-4/M82	0.7272
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	0.96847
3-2/M82	N/A	N/A
4-1-1/M82	1.14439
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	1.06946	1
6-2/M82	0.64414
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	0.92445	0.321
IL2-6/WTpooled	0.83332	0.473
IL7-5/WTpooled	1.74802	0.792
IL7-3/WTpooled	0.23059	0.294
IL12-4/WTpooled	1.25283	0.52
IL1-4/WTpooled	0.80728
WT/WTpooled	0.97107	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	0.8275	0.226

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.98667	1
DC3000/delta hrp 6h	1.02719	1
DC3000/delta hrp 12h	1.21143	1
DC3000/delta hrp 24h	0.45593	0.034

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.46254	0.023
DC3000 delta B/DC3000 delta AB	0.37653	0.02

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.86469	0.265
Exp 36h	0.70405	0.406
Exp 60h	0.72214	0.29

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

hybridization	ratio	FDR (corrected p value)
self-self	1.05138	1
Var 0h	0.96359	1
Var 12h I row2-row1	0.80027	0.338
Var 12h NI row2-row1	0.9687	0.906
Var 36h I row2-row1	0.62689	0.805
Var 36h NI row2-row1	1.21856	0.482
Var 60h I row2-row1	1.32668	0.562
Var 60h NI row2-row1	1.06922	0.904
Time course 0hI-0hNI	1.00257	1
Time course 12hI-12hNI	1.00185	1
Time course 36hI-36hNI	0.99044	0.654
Time course 60hI-60hNI	0.13693	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)	1.23233	0.256
transgenic ySAMdc/azygous control (breaker)	2.84863	0.172
transgenic ySAMdc/azygous control (red)	1.92908	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.72611	0.055

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	2.77061	0.229

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	5.3587	0.083
Manapal/WT (break)	7.67188	0.123
Manapal/WT (red)	12.5291	0.137