Tomato Functional Genomics Database (TFGD)

Expression of 1-1-1.2.17.7

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	1.03622	0.912
27DAP/17DAP	1.1291	0.845
39DAP/27DAP	0.96973	0.719
41DAP/39DAP	1.1117	0.372
42DAP/41DAP	0.87601	1
43DAP/42DAP	1.05073	1
47DAP/43DAP	1.14911	0.733
52DAP/47DAP	0.87875	0.662
57DAP/52DAP	1.03275	0.993

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98508	0.616
17DAP/reference	0.87241	0.024
27DAP/reference	0.96259	0.581
39DAP/reference	0.8935	0.046
41DAP/reference	0.85261	0.01
42DAP/reference	0.99692	0.587
43DAP/reference	0.93269	0.107
47DAP/reference	1.06871	0.318
52DAP/reference	1.24216	0.102
57DAP/reference	1.2031	0.013

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.99951	0.899
27DAP/17DAP	1.00002	1
39DAP/27DAP	0.9903	0.984
41DAP/39DAP	1.04178	0.807
42DAP/41DAP	1.10397	0.635
43DAP/42DAP	1.04223	0.351
47DAP/43DAP	1.01302	0.88
52DAP/47DAP	0.99671	0.97
57DAP/52DAP	0.96439	0.572
57DAP/7DAP	0.88922	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.98009	0.27
17DAP/reference	1.00158	1
27DAP/reference	0.98699	0.402
39DAP/reference	1.02036	0.538
41DAP/reference	1.0744	0.199
42DAP/reference	1.07809	0.1
43DAP/reference	1.04325	0.157
47DAP/reference	1.13238	0.161
52DAP/reference	1.09415	0.052
57DAP/reference	1.09461	0.029

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.87137	0.026
17DAP/reference	0.83746	0.01
27DAP/reference	1.00375	1
39DAP/reference	1.01936	1
41DAP/reference	0.97756	0.459
42DAP/reference	0.98994	0.594
43DAP/reference	0.84975	0.07
47DAP/reference	0.90876	0.107
52DAP/reference	0.95988	0.22
57DAP/reference	0.81614	0.032

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.97168	0.071
17DAP/reference	0.97104	0.381
27DAP/reference	0.98836	0.516
39DAP/reference	1.01893	0.578
41DAP/reference	0.98967	0.56
42DAP/reference	1.10074	0.566
43DAP/reference	1.25634	0.205
47DAP/reference	0.9973	0.667
52DAP/reference	1.00898	0.965
57DAP/reference	1.72439	0.044

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	0.91326	0.961
26DAP/20DAP	0.97761	1
34DAP/26DAP	1.04644	1
51DAP/34DAP	0.99955	0.98
52DAP/51DAP	1.01087	0.86
53DAP/52DAP	0.89012	0.677
55DAP/53DAP	1.12639	0.948
57DAP/55DAP	1.0886	0.764
62DAP/57DAP	0.96643	0.871
68DAP/62DAP	1.12565	0.729
68DAP/14DAP	1.3542	0.063

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

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	1.0064	0.908

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.77792	0.234
Mature Green Tomato/Ripe Tomato	1.09093	0.881
Immature Eggplant/Mature Eggplant	1.72001	0.05
Ripe Pepper/Ripe Tomato	1.26922	1
Mature Eggplant/Ripe Tomato	0.90426	1

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	0.94242	0.944
1-1-2/M82	0.96375	0.958
12-2/M82	0.87387	0.955
12-4/M82	0.97006	0.619
1-3/M82	0.96418	0.501
2-1-1/M82	0.89342	0.784
2-1/M82	1.00712	1
2-6/M82	0.92968	1
3-2/M82	0.99605	1
4-1-1/M82	1.06235	1
4-1/M82	0.90479
4-3-2/M82	0.9214	1
4-3/M82	0.96698	1
5-3/M82	0.99814	1
6-2/M82	0.97317	1
6-3/M82	1.01063	1
7-1/M82	0.98206	0.452
7-2/M82	0.98726	1
9-3-2/M82	0.99371	1

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.27096	0.277
IL2-6/WTpooled	0.9978	1
IL7-5/WTpooled	0.7698	1
IL7-3/WTpooled	1.26014	1
IL12-4/WTpooled	0.98141	1
IL1-4/WTpooled	1.00022	1
WT/WTpooled	0.902	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	1.13027	0.177

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

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	0.99805	1
DC3000/delta hrp 6h	0.97708	0.95
DC3000/delta hrp 12h	N/A	N/A
DC3000/delta hrp 24h	1.00073	1

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	1.24872	0.063
DC3000 delta B/DC3000 delta AB	1.24055	0.137

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

hybridization	ratio	FDR (corrected p value)
Exp 12h	1.04816	1
Exp 36h	0.96542	0.943
Exp 60h	1.12304	0.563

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

hybridization	ratio	FDR (corrected p value)
self-self	0.99585	1
Var 0h	0.80789	1
Var 12h I row2-row1	1.0353	0.795
Var 12h NI row2-row1	0.87888	0.82
Var 36h I row2-row1	0.7848	0.805
Var 36h NI row2-row1	0.95555	0.28
Var 60h I row2-row1	1.25151	0.562
Var 60h NI row2-row1	0.98145	1
Time course 0hI-0hNI	1.00325	1
Time course 12hI-12hNI	1.01636	0.811
Time course 36hI-36hNI	1.04267	0.651
Time course 60hI-60hNI	1.55237	0.012

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)	1.00014	1
transgenic ySAMdc/azygous control (breaker)	1.20614	0.248
transgenic ySAMdc/azygous control (red)	1.05505	0.92

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	N/A	N/A

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

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.74216	0.238

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

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	0.89347	1
Manapal/WT (break)	0.81251	0.333
Manapal/WT (red)	0.72584	0.181