Tomato Functional Genomics Database (TFGD)

Expression of 1-1-2.3.9.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.17687	0.575
27DAP/17DAP	0.84691	0.575
39DAP/27DAP	0.93059	0.631
41DAP/39DAP	0.70807	0.171
42DAP/41DAP	1.3204	0.702
43DAP/42DAP	1.03588	1
47DAP/43DAP	0.95664	0.815
52DAP/47DAP	0.99618	0.693
57DAP/52DAP	0.89224	0.919

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97648	0.55
17DAP/reference	1.14959	0.565
27DAP/reference	1.1187	0.165
39DAP/reference	0.95324	0.611
41DAP/reference	1.01757	0.624
42DAP/reference	0.92126	0.04
43DAP/reference	1.02912	0.596
47DAP/reference	1.00384	0.764
52DAP/reference	0.77427	0.018
57DAP/reference	0.88253	0.138

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.01258	0.99
27DAP/17DAP	0.9066	0.312
39DAP/27DAP	1.06911	0.526
41DAP/39DAP	0.99959	1
42DAP/41DAP	1.01074	1
43DAP/42DAP	1.06173	0.23
47DAP/43DAP	1.00701	1
52DAP/47DAP	1.00098	0.987
57DAP/52DAP	0.99806	0.902
57DAP/7DAP	0.93414	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.23755	0.074
17DAP/reference	1.30028	0.028
27DAP/reference	1.43327	0.013
39DAP/reference	1.52059	0.017
41DAP/reference	1.04148	1
42DAP/reference	0.90952	0.235
43DAP/reference	1.11789	0.188
47DAP/reference	1.11962	0.561
52DAP/reference	0.81296	0.028
57DAP/reference	1.04795	0.698

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.04254	0.776
17DAP/reference	0.87515	0.099
27DAP/reference	0.89511	0.15
39DAP/reference	0.91847	0.221
41DAP/reference	0.88467	0.277
42DAP/reference	0.93216	0.212
43DAP/reference	0.81709	0.132
47DAP/reference	0.88759	0.102
52DAP/reference	0.84229	0.023
57DAP/reference	0.77346	0.007

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.40386	0.035
17DAP/reference	0.99211	0.696
27DAP/reference	1.23813	0.26
39DAP/reference	1.35992	0.037
41DAP/reference	1.09089	0.57
42DAP/reference	1.14673	0.391
43DAP/reference	1.13799	1
47DAP/reference	0.89166	0.174
52DAP/reference	1.36367	0.212
57DAP/reference	0.86877	0.165

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.14015	0.85
26DAP/20DAP	1.02135	1
34DAP/26DAP	1.02566	1
51DAP/34DAP	0.94439	0.513
52DAP/51DAP	1.03653	0.606
53DAP/52DAP	1.06124
55DAP/53DAP	1.26314
57DAP/55DAP	1.18264	0.249
62DAP/57DAP	1.33488	0.678
68DAP/62DAP	0.69492	0.505
68DAP/14DAP	0.56424	0.078

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.90033	0.108

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	9.80254	0.058
Mature Green Tomato/Ripe Tomato	50.5005	0.363
Immature Eggplant/Mature Eggplant	0.69755	0.062
Ripe Pepper/Ripe Tomato	0.5222	0.224
Mature Eggplant/Ripe Tomato	3.61075	0.26

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.10396	0.877
1-1-2/M82	0.92346	1
12-2/M82	0.93059	0.955
12-4/M82	1.39591	1
1-3/M82	1.07771	1
2-1-1/M82	1.68697	0.375
2-1/M82	0.79721
2-6/M82	1.39377	0.505
3-2/M82	1.22447	0.463
4-1-1/M82	0.91062	1
4-1/M82	N/A	N/A
4-3-2/M82	N/A	N/A
4-3/M82	0.72067
5-3/M82	0.81038	0.642
6-2/M82	1.42381	1
6-3/M82	0.82405	1
7-1/M82	N/A	N/A
7-2/M82	1.16863	1
9-3-2/M82	N/A	N/A

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	0.97838	1
IL2-6/WTpooled	1.04075	0.659
IL7-5/WTpooled	1.49141
IL7-3/WTpooled	0.88966	0.418
IL12-4/WTpooled	0.99479	1
IL1-4/WTpooled	1.01842	0.426
WT/WTpooled	0.94474	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	0.88672	0.975

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.01653	1
DC3000/delta hrp 6h	1.00469	0.95
DC3000/delta hrp 12h	0.79612	1
DC3000/delta hrp 24h	1.12978	0.296

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	0.99658	1
DC3000 delta B/DC3000 delta AB	1.06547	0.462

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.78083	1
Exp 36h	0.89085	0.661
Exp 60h	0.94718	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99172	1
Var 0h	0.96916	1
Var 12h I row2-row1	1.03949	1
Var 12h NI row2-row1	0.87446	0.82
Var 36h I row2-row1	0.85191	0.34
Var 36h NI row2-row1	0.79797	0.706
Var 60h I row2-row1	1.2404	0.562
Var 60h NI row2-row1	1.42981	0.904
Time course 0hI-0hNI	1.16061	0.63
Time course 12hI-12hNI	1.01999	0.861
Time course 36hI-36hNI	0.89041	0.076
Time course 60hI-60hNI	1.00017	1

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)	0.98772	0.789
transgenic ySAMdc/azygous control (breaker)	0.48427	0.137
transgenic ySAMdc/azygous control (red)	1.17165	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02316	1

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.01104	1

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.37444	0.105
Manapal/WT (break)	1.09429	1
Manapal/WT (red)	0.7983	0.229