Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.10.4

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.83435	0.31
27DAP/17DAP	1.15186	0.847
39DAP/27DAP	0.88106	0.583
41DAP/39DAP	1.52993	0.386
42DAP/41DAP	0.92088	1
43DAP/42DAP	0.94812	0.892
47DAP/43DAP	1.29933	0.527
52DAP/47DAP	0.99759	0.828
57DAP/52DAP	1.06749	1

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88137	0.067
17DAP/reference	1.1447	0.066
27DAP/reference	1.03556	0.75
39DAP/reference	1.085	0.486
41DAP/reference	1.01272	1
42DAP/reference	0.88559	0.041
43DAP/reference	0.87119	0.163
47DAP/reference	0.95037	0.345
52DAP/reference	0.9652	0.461
57DAP/reference	0.88383	0.106

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.86167	0.644
27DAP/17DAP	N/A	N/A
39DAP/27DAP	0.92349	0.775
41DAP/39DAP	1.04007	1
42DAP/41DAP	0.93243	0.666
43DAP/42DAP	1.52529	0.176
47DAP/43DAP	0.97808	0.954
52DAP/47DAP	1.27194
57DAP/52DAP	0.91112	0.463
57DAP/7DAP	N/A	N/A

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.89166	0.296
17DAP/reference	1.31897	0.042
27DAP/reference	1.08838	0.16
39DAP/reference	0.83064	0.023
41DAP/reference	0.80647	0.139
42DAP/reference	0.6532	0.018
43DAP/reference	1.12431	0.289
47DAP/reference	0.95543	0.504
52DAP/reference	0.9294	0.254
57DAP/reference	1.21484	0.094

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.16087	0.22
17DAP/reference	0.86362	0.389
27DAP/reference	0.99002	0.598
39DAP/reference	0.82391	0.105
41DAP/reference	0.89416	0.218
42DAP/reference	0.99014	0.594
43DAP/reference	1.27998	0.117
47DAP/reference	0.94669	0.277
52DAP/reference	0.93445	0.327
57DAP/reference	1.06133	0.786

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97999	0.489
17DAP/reference	1.11194	0.578
27DAP/reference	1.61099	0.02
39DAP/reference	1.28536	0.024
41DAP/reference	1.10299	0.605
42DAP/reference	1.15301	0.154
43DAP/reference	0.90259	0.179
47DAP/reference	0.94632	0.421
52DAP/reference	1.13916	0.247
57DAP/reference	0.82264	0.062

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.54577	0.966
26DAP/20DAP	0.93384	1
34DAP/26DAP	1.03105	1
51DAP/34DAP	0.60296	0.136
52DAP/51DAP	1.00072	1
53DAP/52DAP	1.51908	0.608
55DAP/53DAP	0.99261	0.886
57DAP/55DAP	0.82075	0.256
62DAP/57DAP	1.20759	0.8
68DAP/62DAP	1.09061	0.834
68DAP/14DAP	0.66384	0.375

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.81374	0.253

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	N/A	N/A
Ripe Pepper/Ripe Tomato	N/A	N/A
Mature Eggplant/Ripe Tomato	N/A	N/A

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	1.05045
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	0.93973	1
3-2/M82	N/A	N/A
4-1-1/M82	0.51468
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	0.6334	1
6-2/M82	0.56295
6-3/M82	1.02747
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	1.1384	0.493
IL2-6/WTpooled	1.07118	0.788
IL7-5/WTpooled	0.92446
IL7-3/WTpooled	0.88104	0.31
IL12-4/WTpooled	0.87211	0.71
IL1-4/WTpooled	0.88712	0.699
WT/WTpooled	1.0071	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	0.76687

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05471	0.914
DC3000/delta hrp 6h	N/A	N/A
DC3000/delta hrp 12h	1.00236	1
DC3000/delta hrp 24h	1.11799	0.535

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	1.03596	1
Var 0h	1.03776	0.936
Var 12h I row2-row1	1.16245
Var 12h NI row2-row1	0.90728	0.82
Var 36h I row2-row1	0.97759
Var 36h NI row2-row1	0.93835	0.225
Var 60h I row2-row1	1.08666	0.562
Var 60h NI row2-row1	0.93321	0.298
Time course 0hI-0hNI	1.09533	0.852
Time course 12hI-12hNI	1.04667	0.816
Time course 36hI-36hNI	1.09427	0.799
Time course 60hI-60hNI	1.20281	0.575

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)	0.97059	0.614
transgenic ySAMdc/azygous control (breaker)	0.98963	1
transgenic ySAMdc/azygous control (red)	0.99836	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.95553	0.09

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.83961	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.14537	1
Manapal/WT (break)	0.74815	0.333
Manapal/WT (red)	N/A	N/A