Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.3.9.13

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.0471	0.847
27DAP/17DAP	1.2388	0.808
39DAP/27DAP	0.83305	0.529
41DAP/39DAP	2.05581	0.285
42DAP/41DAP	1.48607	0.752
43DAP/42DAP	0.97506	0.918
47DAP/43DAP	1.04672	0.949
52DAP/47DAP	1.42032	0.538
57DAP/52DAP	0.8748	0.889

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98945	0.661
17DAP/reference	0.99856	1
27DAP/reference	0.98286	0.654
39DAP/reference	0.93524	0.159
41DAP/reference	1.06639	0.287
42DAP/reference	0.99255	0.517
43DAP/reference	1.03703	0.569
47DAP/reference	0.90984	0.014
52DAP/reference	0.67914	0.026
57DAP/reference	0.85618	0.034

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94148	0.526
27DAP/17DAP	1.00518	0.969
39DAP/27DAP	1.14887	0.436
41DAP/39DAP	1.06832	0.781
42DAP/41DAP	0.96434	0.746
43DAP/42DAP	1.01389	1
47DAP/43DAP	0.96553	0.781
52DAP/47DAP	1.08035	0.785
57DAP/52DAP	1.03811	0.8
57DAP/7DAP	1.26216	0.249

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87495	0.073
17DAP/reference	0.86669	0.012
27DAP/reference	0.91137	0.026
39DAP/reference	0.85611	0.011
41DAP/reference	0.77054	0.026
42DAP/reference	0.73785	0.011
43DAP/reference	0.82317	0.064
47DAP/reference	0.87967	0.383
52DAP/reference	0.82083	0.097
57DAP/reference	0.76102	0.023

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.2422	0.049
17DAP/reference	1.04705	0.613
27DAP/reference	0.88376	0.195
39DAP/reference	0.79011	0.108
41DAP/reference	0.80741	0.045
42DAP/reference	0.76766	0.022
43DAP/reference	1.15742	0.161
47DAP/reference	0.88736	0.053
52DAP/reference	0.99583	0.619
57DAP/reference	1.43789	0.066

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.95556	0.147
17DAP/reference	0.9625	0.537
27DAP/reference	0.89119	0.067
39DAP/reference	0.92203	0.025
41DAP/reference	0.88691	0.04
42DAP/reference	0.87843	0.22
43DAP/reference	0.84911	0.171
47DAP/reference	1.00767	0.687
52DAP/reference	1.05516	0.749
57DAP/reference	0.59657	0.059

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.96099	1
26DAP/20DAP	0.92703	0.512
34DAP/26DAP	1.06534	1
51DAP/34DAP	1.01013	0.988
52DAP/51DAP	1.03954	0.904
53DAP/52DAP	N/A	N/A
55DAP/53DAP	1.15271
57DAP/55DAP	1.24751	0.301
62DAP/57DAP	1.21413	0.217
68DAP/62DAP	0.78219	0.109
68DAP/14DAP	1.04438	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.04826	0.865

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	1.4247	0.058
Mature Green Tomato/Ripe Tomato	1.06879	0.66
Immature Eggplant/Mature Eggplant	1.01162	1
Ripe Pepper/Ripe Tomato	1.70008	0.258
Mature Eggplant/Ripe Tomato	1.19319	0.373

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.97823	0.944
1-1-2/M82	0.96776	1
12-2/M82	1.00123	1
12-4/M82	0.82651	0.619
1-3/M82	0.82052	0.33
2-1-1/M82	1.0293	1
2-1/M82	1.21075
2-6/M82	1.21066	0.594
3-2/M82	0.89454	1
4-1-1/M82	1.00016	1
4-1/M82	0.77956	1
4-3-2/M82	1.07175	0.246
4-3/M82	0.99305	1
5-3/M82	0.93166	0.642
6-2/M82	1.0357
6-3/M82	1.01107
7-1/M82	N/A	N/A
7-2/M82	0.98576	1
9-3-2/M82	0.94233	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
IL2-6/WTpooled	0.88025	1
IL7-5/WTpooled	N/A	N/A
IL7-3/WTpooled	1.05789	1
IL12-4/WTpooled	1.63442	0.516
IL1-4/WTpooled	1.02727	1
WT/WTpooled	1.0193	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	1.04848	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.02918	0.921
DC3000/delta hrp 6h	1.0276	1
DC3000/delta hrp 12h	1.46276	1
DC3000/delta hrp 24h	1.10807	0.383

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.15348
DC3000 delta B/DC3000 delta AB	1.06352	0.484

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.11188	0.254
Exp 36h	N/A	N/A
Exp 60h	1.18943	0.283

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

hybridization	ratio	FDR (corrected p value)
self-self	0.98426	1
Var 0h	1.1567	0.421
Var 12h I row2-row1	1.1585	0.324
Var 12h NI row2-row1	0.9254	0.546
Var 36h I row2-row1	0.97123	1
Var 36h NI row2-row1	1.01659	1
Var 60h I row2-row1	1.19928	1
Var 60h NI row2-row1	1.24024	0.904
Time course 0hI-0hNI	1.08044	0.662
Time course 12hI-12hNI	1.07705	0.493
Time course 36hI-36hNI	1.02588	0.722
Time course 60hI-60hNI	1.22123	0.01

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)	0.91778	0.265
transgenic ySAMdc/azygous control (breaker)	0.81037	0.142
transgenic ySAMdc/azygous control (red)	0.94327	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.0301	0.135

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.97978	0.59

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.96126	1
Manapal/WT (break)	0.86862	0.333
Manapal/WT (red)	0.80123	0.315