Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.2.2.18

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.2461	0.115
27DAP/17DAP	1.05471	1
39DAP/27DAP	0.93325	0.631
41DAP/39DAP	0.98552	0.941
42DAP/41DAP	1.19407	0.578
43DAP/42DAP	1.02308	0.937
47DAP/43DAP	1.04603	0.842
52DAP/47DAP	0.87211	0.637
57DAP/52DAP	1.1738	0.907

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98113	0.589
17DAP/reference	0.80993	0.046
27DAP/reference	0.92235	0.314
39DAP/reference	0.87868	0.128
41DAP/reference	0.71218	0.009
42DAP/reference	0.90431	0.035
43DAP/reference	0.92461	0.394
47DAP/reference	0.99301	0.568
52DAP/reference	0.98506	0.53
57DAP/reference	1.22333	0.011

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.36902	0.271
27DAP/17DAP	1.01719	1
39DAP/27DAP	1.01267	0.845
41DAP/39DAP	1.02612	1
42DAP/41DAP	1.04259	0.991
43DAP/42DAP	1.07324	0.413
47DAP/43DAP	0.9154	0.382
52DAP/47DAP	1.06562	0.804
57DAP/52DAP	0.93528	0.665
57DAP/7DAP	0.63176	0.219

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88091	0.138
17DAP/reference	0.95982	0.447
27DAP/reference	1.00843	0.698
39DAP/reference	1.15879	0.436
41DAP/reference	0.88935	0.311
42DAP/reference	0.95212	0.04
43DAP/reference	0.96436	0.292
47DAP/reference	0.98148	0.671
52DAP/reference	1.06518	0.636
57DAP/reference	1.02123	0.907

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.76346	0.012
17DAP/reference	0.82393	0.021
27DAP/reference	0.94246	0.269
39DAP/reference	0.8622	0.119
41DAP/reference	0.79117	0.044
42DAP/reference	0.86576	0.055
43DAP/reference	1.09194	0.704
47DAP/reference	0.93243	0.097
52DAP/reference	0.87591	0.025
57DAP/reference	0.85064	0.068

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12681	0.532
17DAP/reference	1.11831	0.631
27DAP/reference	1.16065	0.12
39DAP/reference	1.06015	0.227
41DAP/reference	1.23332	0.056
42DAP/reference	1.23152	0.142
43DAP/reference	1.09947	0.815
47DAP/reference	0.88723	0.089
52DAP/reference	1.13023	0.436
57DAP/reference	1.05873	0.371

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.06258	0.966
26DAP/20DAP	0.9003	1
34DAP/26DAP	1.12186	1
51DAP/34DAP	1.37631	0.177
52DAP/51DAP	0.93166	1
53DAP/52DAP	1.04043	1
55DAP/53DAP	0.83547	0.293
57DAP/55DAP	0.99732	0.938
62DAP/57DAP	1.18249	0.833
68DAP/62DAP	0.99993	0.885
68DAP/14DAP	1.44695	0.2

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.73936	0.108

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.70164	0.203
Mature Green Tomato/Ripe Tomato	1.15686	0.437
Immature Eggplant/Mature Eggplant	0.77024	0.1
Ripe Pepper/Ripe Tomato	0.95205	1
Mature Eggplant/Ripe Tomato	0.99484	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.28384	0.742
1-1-2/M82	1.15211	1
12-2/M82	0.93599	0.955
12-4/M82	0.85542	1
1-3/M82	0.69	0.378
2-1-1/M82	1.11376	0.764
2-1/M82	1.29215	0.345
2-6/M82	0.85673	1
3-2/M82	1.1174
4-1-1/M82	0.99728	1
4-1/M82	1.07078	1
4-3-2/M82	0.95226	1
4-3/M82	1.03488	1
5-3/M82	0.99132	1
6-2/M82	0.75893	1
6-3/M82	0.94364	1
7-1/M82	N/A	N/A
7-2/M82	0.8045	0.578
9-3-2/M82	0.89673	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.88787	0.473
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.37431	0.362
IL12-4/WTpooled	1.16111	0.695
IL1-4/WTpooled	N/A	N/A
WT/WTpooled	1.06373	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	0.81651	0.75

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.93777	0.642
DC3000/delta hrp 6h	1.05539	1
DC3000/delta hrp 12h	0.94508	1
DC3000/delta hrp 24h	0.82598	0.126

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	0.34909	0.022

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.01112	1
Exp 36h	1.15853	0.693
Exp 60h	1.04004	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99053	1
Var 0h	1.00443	1
Var 12h I row2-row1	0.70256	0.363
Var 12h NI row2-row1	1.09419
Var 36h I row2-row1	0.95806	1
Var 36h NI row2-row1	1.66508
Var 60h I row2-row1	1.11303
Var 60h NI row2-row1	N/A	N/A
Time course 0hI-0hNI	1.00747	1
Time course 12hI-12hNI	0.94721	0.511
Time course 36hI-36hNI	0.8411	0.047
Time course 60hI-60hNI	0.33251	0.006

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)	0.98214	0.391
transgenic ySAMdc/azygous control (breaker)	1.32169	0.178
transgenic ySAMdc/azygous control (red)	1.03083	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.91183	0.072

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	1.38291	0.237

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.1923	0.14
Manapal/WT (break)	0.91997	1
Manapal/WT (red)	1.11547	0.413