Tomato Functional Genomics Database (TFGD)

Expression of 1-1-4.3.10.12

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.22417	0.63
27DAP/17DAP	0.87627	0.749
39DAP/27DAP	1.13338	0.677
41DAP/39DAP	0.97579	0.841
42DAP/41DAP	0.8487	1
43DAP/42DAP	0.88526	0.705
47DAP/43DAP	1.25072	0.391
52DAP/47DAP	1.01028	0.908
57DAP/52DAP	1.34298	0.656

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.18673	0.065
17DAP/reference	0.96906	0.567
27DAP/reference	0.90243	0.286
39DAP/reference	0.98323	0.75
41DAP/reference	0.97252	0.667
42DAP/reference	0.90665	0.139
43DAP/reference	1.0012	0.904
47DAP/reference	1.09852	0.558
52DAP/reference	1.07205	0.663
57DAP/reference	1.1151	0.028

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.04507	0.899
27DAP/17DAP	0.8913	0.537
39DAP/27DAP	0.87173	0.3
41DAP/39DAP	1.02503	1
42DAP/41DAP	0.9749	0.777
43DAP/42DAP	0.91583	0.431
47DAP/43DAP	0.96135	0.75
52DAP/47DAP	0.79187	0.179
57DAP/52DAP	0.84166	0.084
57DAP/7DAP	0.46945	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.1871	0.076
17DAP/reference	0.93717	0.22
27DAP/reference	1.06447	0.301
39DAP/reference	0.96881	0.474
41DAP/reference	1.09678	0.27
42DAP/reference	0.93953	0.304
43DAP/reference	1.05224	0.83
47DAP/reference	1.18035	0.187
52DAP/reference	0.97538	0.477
57DAP/reference	0.9402	0.341

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.36274	0.053
17DAP/reference	1.09064	0.824
27DAP/reference	1.39722	0.068
39DAP/reference	1.17636	0.324
41DAP/reference	0.99631	0.557
42DAP/reference	1.0605	0.61
43DAP/reference	1.21261	0.522
47DAP/reference	0.9135	0.149
52DAP/reference	0.97936	0.576
57DAP/reference	0.89058	0.18

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04943	0.809
17DAP/reference	1.32407	0.427
27DAP/reference	0.98631	0.657
39DAP/reference	1.06303	0.406
41DAP/reference	1.09384	0.213
42DAP/reference	1.03129	0.877
43DAP/reference	1.07371	0.71
47DAP/reference	1.0441	0.754
52DAP/reference	1.01544	0.99
57DAP/reference	1.00391	0.801

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.00133	1
26DAP/20DAP	1.35095	0.598
34DAP/26DAP	0.71675	0.152
51DAP/34DAP	0.89547	0.681
52DAP/51DAP	1.04534	0.638
53DAP/52DAP	1.03147	1
55DAP/53DAP	1.06466	0.925
57DAP/55DAP	0.85251	0.496
62DAP/57DAP	0.92261	0.871
68DAP/62DAP	0.95323	0.787
68DAP/14DAP	1.39779	0.676

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	2.99785	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	1.04868	1
Immature Eggplant/Mature Eggplant	1.26581	0.069
Ripe Pepper/Ripe Tomato	0.54667	0.224
Mature Eggplant/Ripe Tomato	1.09005	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.02799	0.877
1-1-2/M82	1.24426	1
12-2/M82	0.95292
12-4/M82	1.09915	1
1-3/M82	0.9925	1
2-1-1/M82	1.39504	0.375
2-1/M82	N/A	N/A
2-6/M82	0.95709	1
3-2/M82	1.00151	1
4-1-1/M82	0.92187	1
4-1/M82	0.75216
4-3-2/M82	1.04289	1
4-3/M82	N/A	N/A
5-3/M82	1.11425	0.572
6-2/M82	0.99125
6-3/M82	1.02284
7-1/M82	N/A	N/A
7-2/M82	0.93684	0.469
9-3-2/M82	1.80143	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	1.05849	0.584
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.21219	1
IL12-4/WTpooled	0.96893	1
IL1-4/WTpooled	1.41018	1
WT/WTpooled	1.04277	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	0.97783	1

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01308	0.921
DC3000/delta hrp 6h	0.95354	0.95
DC3000/delta hrp 12h	0.98228	1
DC3000/delta hrp 24h	1.05774	0.673

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.03089	0.441
DC3000 delta B/DC3000 delta AB	1.04748	0.586

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.94768	0.265
Exp 36h	1.07485	1
Exp 60h	1.22317	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07832	1
Var 0h	1.07462	0.936
Var 12h I row2-row1	1.01221	1
Var 12h NI row2-row1	1.19054	0.281
Var 36h I row2-row1	0.80115	1
Var 36h NI row2-row1	0.90504	0.706
Var 60h I row2-row1	0.87939	0.439
Var 60h NI row2-row1	0.89306	0.756
Time course 0hI-0hNI	0.88704	0.181
Time course 12hI-12hNI	1.08952	0.25
Time course 36hI-36hNI	1.03188	0.975
Time course 60hI-60hNI	0.96616	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)	0.92315	0.348
transgenic ySAMdc/azygous control (breaker)	0.9097	0.49
transgenic ySAMdc/azygous control (red)	0.88724	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.08694	0.037

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91276	0.35

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.87521	1
Manapal/WT (break)	1.16027	1
Manapal/WT (red)	2.34969	0.222