Tomato Functional Genomics Database (TFGD)

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Expression of 1-1-3.3.7.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.92405	0.596
27DAP/17DAP	1.16881	0.808
39DAP/27DAP	1.02773	0.899
41DAP/39DAP	1.29367	0.478
42DAP/41DAP	0.95891	1
43DAP/42DAP	1.07914	1
47DAP/43DAP	1.0102	0.92
52DAP/47DAP	1.36286	0.545
57DAP/52DAP	0.8364	0.82

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.21103	0.065
17DAP/reference	1.315	0.015
27DAP/reference	1.21166	0.075
39DAP/reference	1.309	0.038
41DAP/reference	1.2888	0.079
42DAP/reference	1.24691	0.003
43DAP/reference	1.03137	0.928
47DAP/reference	1.14661	0.048
52DAP/reference	1.2464	0.088
57DAP/reference	0.9556	0.221

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.90854	0.496
27DAP/17DAP	1.05342	0.909
39DAP/27DAP	1.08793	0.429
41DAP/39DAP	1.14602	0.727
42DAP/41DAP	0.95984	0.69
43DAP/42DAP	1.15572	0.192
47DAP/43DAP	1.07338	0.765
52DAP/47DAP	1.07601	0.776
57DAP/52DAP	0.95537	0.605
57DAP/7DAP	1.08611	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.83377	0.1
17DAP/reference	0.90741	0.167
27DAP/reference	1.01041	1
39DAP/reference	0.81131	0.012
41DAP/reference	0.87276	0.133
42DAP/reference	0.96072	0.211
43DAP/reference	0.72618	0.015
47DAP/reference	0.90445	0.293
52DAP/reference	0.70438	0.012
57DAP/reference	0.77493	0.01

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.12505	0.289
17DAP/reference	1.4588	0.028
27DAP/reference	1.24323	0.097
39DAP/reference	1.38827	0.019
41DAP/reference	1.4417	0.112
42DAP/reference	1.33154	0.041
43DAP/reference	1.52328	0.057
47DAP/reference	1.10723	0.084
52DAP/reference	1.25876	0.006
57DAP/reference	1.43098	0.029

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.80245	0.063
17DAP/reference	1.15683	0.641
27DAP/reference	0.80431	0.046
39DAP/reference	0.90553	0.222
41DAP/reference	1.05822	0.961
42DAP/reference	0.96406	0.552
43DAP/reference	0.95273	0.449
47DAP/reference	1.35026	0.008
52DAP/reference	0.81392	0.174
57DAP/reference	1.34061	0.279

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.80127	1
26DAP/20DAP	0.98044	1
34DAP/26DAP	1.24139	0.819
51DAP/34DAP	1.11741	0.597
52DAP/51DAP	1.15324	0.281
53DAP/52DAP	1.09357	0.868
55DAP/53DAP	1.05485	1
57DAP/55DAP	1.00052	0.961
62DAP/57DAP	0.88765	0.681
68DAP/62DAP	0.9044	0.722
68DAP/14DAP	0.81168	1

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	0.96806	0.576

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	N/A	N/A
Mature Green Tomato/Ripe Tomato	0.92414	0.522
Immature Eggplant/Mature Eggplant	5.99885	N/A
Ripe Pepper/Ripe Tomato	0.29278	0.224
Mature Eggplant/Ripe Tomato	0.50424	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.11709	0.591
1-1-2/M82	1.12467	1
12-2/M82	1.45356	0.336
12-4/M82	1.24911	1
1-3/M82	0.83427	0.441
2-1-1/M82	0.85434	0.465
2-1/M82	1.32257	N/A
2-6/M82	0.86662	0.501
3-2/M82	N/A	N/A
4-1-1/M82	0.81301	1
4-1/M82	0.48657	N/A
4-3-2/M82	1.36378	N/A
4-3/M82	0.89362	0.611
5-3/M82	1.07648	1
6-2/M82	0.57302	N/A
6-3/M82	0.92563	1
7-1/M82	0.94087	1
7-2/M82	0.84358	0.796
9-3-2/M82	0.99323	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	N/A	N/A
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	N/A	N/A
WT/WTpooled	0.98558	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	1.1482	0.853

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.05967	0.921
DC3000/delta hrp 6h	1.38711	1
DC3000/delta hrp 12h	1.0704	1
DC3000/delta hrp 24h	0.88871	0.19

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.44373	0.29
DC3000 delta B/DC3000 delta AB	1.45453	0.265

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.95191	1
Exp 36h	1.19157	1
Exp 60h	0.95527	0.855

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

hybridization	ratio	FDR (corrected p value)
self-self	1.07607	1
Var 0h	1.30146	0.782
Var 12h I row2-row1	1.20379	0.296
Var 12h NI row2-row1	0.76027	0.494
Var 36h I row2-row1	0.86935	0.575
Var 36h NI row2-row1	0.88883	0.522
Var 60h I row2-row1	1.18984	0.562
Var 60h NI row2-row1	1.41866	0.904
Time course 0hI-0hNI	1.05544	0.719
Time course 12hI-12hNI	1.0548	0.687
Time course 36hI-36hNI	1.01357	0.881
Time course 60hI-60hNI	1.15326	0.115

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)	0.98089	0.789
transgenic ySAMdc/azygous control (breaker)	0.99404	1
transgenic ySAMdc/azygous control (red)	1.1381	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	0.9329	0.117

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.86675	0.255

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.95696	1
Manapal/WT (break)	0.91061	1
Manapal/WT (red)	0.74564	0.188