Tomato Functional Genomics Database (TFGD)

Expression of 1-1-3.2.16.21

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85206	0.395
27DAP/17DAP	0.67168	0.095
39DAP/27DAP	1.18686	0.588
41DAP/39DAP	1.04944	0.938
42DAP/41DAP	1.01136	1
43DAP/42DAP	0.98727	0.937
47DAP/43DAP	0.99329	0.794
52DAP/47DAP	1.52025	0.43
57DAP/52DAP	1.17635	0.568

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.85756	0.05
17DAP/reference	0.86117	0.041
27DAP/reference	0.97258	0.552
39DAP/reference	0.9013	0.022
41DAP/reference	0.83572	0.049
42DAP/reference	0.95442	0.163
43DAP/reference	0.91722	0.058
47DAP/reference	1.13267	0.096
52DAP/reference	1.33336	0.031
57DAP/reference	1.26228	0.014

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.70253	0.131
27DAP/17DAP	1.5544	0.413
39DAP/27DAP	1.14643	0.548
41DAP/39DAP	1.37561	0.439
42DAP/41DAP	0.81008	0.453
43DAP/42DAP	1.79781	0.019
47DAP/43DAP	1.4385	0.033
52DAP/47DAP	0.99044	0.941
57DAP/52DAP	0.80191	0.272
57DAP/7DAP	1.20085	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88584	0.168
17DAP/reference	0.84951	0.025
27DAP/reference	0.99474	0.656
39DAP/reference	1.04614	1
41DAP/reference	0.83495	0.034
42DAP/reference	1.06629	0.534
43DAP/reference	0.87407	0.159
47DAP/reference	0.99752	1
52DAP/reference	0.96465	0.435
57DAP/reference	0.63869	0.018

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.24563	0.634
17DAP/reference	0.68731	0.004
27DAP/reference	0.86016	0.074
39DAP/reference	0.88159	0.105
41DAP/reference	1.05656	0.749
42DAP/reference	0.95507	0.355
43DAP/reference	0.91514	0.328
47DAP/reference	0.88742	0.013
52DAP/reference	0.87595	0.023
57DAP/reference	0.7209	0.006

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.26675	0.038
17DAP/reference	0.96586	0.601
27DAP/reference	0.87992	0.195
39DAP/reference	0.9454	0.299
41DAP/reference	0.91022	0.185
42DAP/reference	1.05854	0.701
43DAP/reference	0.92449	0.281
47DAP/reference	0.95629	0.286
52DAP/reference	0.85912	0.102
57DAP/reference	1.16022	0.401

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.97503	1
26DAP/20DAP	1.19579
34DAP/26DAP	0.9393	0.92
51DAP/34DAP	1.30152	0.936
52DAP/51DAP	0.78502	1
53DAP/52DAP	1.87787	0.444
55DAP/53DAP	0.93723	0.709
57DAP/55DAP	1.13738	0.666
62DAP/57DAP	0.96431	0.871
68DAP/62DAP	1.2068	0.565
68DAP/14DAP	1.12495	0.676

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.44372	0.663

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.76849	0.377
Immature Eggplant/Mature Eggplant	3.19813	0.05
Ripe Pepper/Ripe Tomato	0.29236	0.224
Mature Eggplant/Ripe Tomato	0.44568	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.01241	1
1-1-2/M82	1.61288	1
12-2/M82	1.4188	0.405
12-4/M82	1.18069	1
1-3/M82	1.01502	1
2-1-1/M82	0.89377	0.465
2-1/M82	0.52022	0.322
2-6/M82	0.97422	1
3-2/M82	N/A	N/A
4-1-1/M82	1.85935	0.966
4-1/M82	1.4407	0.466
4-3-2/M82	N/A	N/A
4-3/M82	1.27617	1
5-3/M82	1.15067	1
6-2/M82	0.86397	1
6-3/M82	0.99761	1
7-1/M82	1.8179
7-2/M82	0.63353	0.553
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.82498	0.277
IL2-6/WTpooled	N/A	N/A
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	N/A	N/A
IL12-4/WTpooled	N/A	N/A
IL1-4/WTpooled	0.76211	0.402
WT/WTpooled	N/A	N/A

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	1.6445	0.699

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.14877	0.914
DC3000/delta hrp 6h	1.10336	1
DC3000/delta hrp 12h	0.95755	1
DC3000/delta hrp 24h	0.89136	0.292

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	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	0.86326
Var 0h	0.98479	1
Var 12h I row2-row1	1.10256	0.58
Var 12h NI row2-row1	0.92109	0.438
Var 36h I row2-row1	0.97195
Var 36h NI row2-row1	0.6534	0.584
Var 60h I row2-row1	1.17182	1
Var 60h NI row2-row1	0.54242	0.292
Time course 0hI-0hNI	0.97827	0.935
Time course 12hI-12hNI	1.12062	0.403
Time course 36hI-36hNI	0.95596	0.484
Time course 60hI-60hNI	0.63477	0.319

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)	0.99298	0.529
transgenic ySAMdc/azygous control (breaker)	0.64474	0.137
transgenic ySAMdc/azygous control (red)	0.96366	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.99478	0.757

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.91177	0.268

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	N/A	N/A
Manapal/WT (break)	0.70218	0.299
Manapal/WT (red)	0.52688	0.181